Chronic diarrhea is more than inconvenient — it’s your body signaling that something in your digestive system isn’t working right. The causes range from food intolerances and infections to autoimmune conditions, thyroid dysfunction, and malabsorption disorders. Left unaddressed, chronic diarrhea can lead to nutritional deficiencies, dehydration, and significant impacts on quality of life.

What many people don’t realize is that blood tests can provide valuable clues about the cause of chronic diarrhea. While stool tests and imaging may also be needed, blood testing can identify inflammation, autoimmune conditions, thyroid dysfunction, nutritional deficiencies from malabsorption, and other conditions that cause or contribute to persistent digestive problems.

Understanding what’s causing your diarrhea is the first step toward resolving it. This article explores the common causes of chronic diarrhea and what blood tests can reveal about each.

Understanding Diarrhea

Diarrhea is defined as loose, watery stools occurring three or more times per day, or a significant increase in stool frequency and looseness from a person’s baseline. But not all diarrhea is the same — the pattern, duration, characteristics, and associated symptoms provide important diagnostic clues that help narrow down the cause.

Acute versus chronic diarrhea:

Acute diarrhea lasts less than two weeks and is usually caused by:

• Viral gastroenteritis (“stomach flu” or “stomach bug”) — the most common cause by far, caused by norovirus, rotavirus, and other viruses
• Bacterial infections (food poisoning) — Salmonella, E. coli, Campylobacter, Shigella, often from contaminated food or water
• Parasitic infections — Giardia, Cryptosporidium, more common in travelers or from contaminated water
• Medication side effects — antibiotics commonly cause diarrhea, as do many other medications
• Dietary indiscretion — eating something that doesn’t agree with you, excessive alcohol, unusual foods

Acute diarrhea usually resolves on its own with supportive care — staying hydrated, resting, and letting the gut recover. Most cases don’t require extensive workup unless there are concerning features: severe symptoms, high fever, bloody stool, signs of dehydration, or immunocompromised status.

Chronic diarrhea persists for four weeks or longer, or recurs repeatedly over an extended period. This is when investigation becomes important, because chronic diarrhea usually has an underlying cause that won’t simply resolve on its own. Chronic diarrhea affects an estimated 5% of the population at any given time and significantly impacts quality of life — it’s not just uncomfortable, it can affect work, social activities, travel, and mental health.

Persistent diarrhea lasts two to four weeks — a middle category. It may be a prolonged acute episode that will eventually resolve, or it may be transitioning to chronic diarrhea. If diarrhea reaches the two-week mark, it’s worth starting to think about possible causes beyond simple infection.

Types of chronic diarrhea:

Understanding the type of diarrhea helps narrow down the cause significantly:

Watery diarrhea: Large-volume, watery stools without blood or pus. This is the most common type and can be further divided into:

• Osmotic diarrhea: Caused by poorly absorbed substances in the gut that draw water in by osmosis. The diarrhea improves or stops with fasting (because the offending substances aren’t being consumed). Examples include lactose intolerance, fructose malabsorption, sugar alcohols (sorbitol, xylitol), and magnesium-containing antacids or supplements.
• Secretory diarrhea: The intestine actively secretes fluid regardless of what you eat. Diarrhea persists even with fasting. Stool volumes are often large (more than a liter daily). Examples include some infections, hormone-secreting tumors (carcinoid, VIPoma), bile acid malabsorption, and some medications.

Fatty diarrhea (steatorrhea): Greasy, foul-smelling, pale stools that may float and are difficult to flush. Often leaves an oily film in the toilet. Indicates fat malabsorption — fat isn’t being properly digested or absorbed. Examples include celiac disease, chronic pancreatitis (insufficient digestive enzymes), bile acid deficiency, small intestinal bacterial overgrowth, and short bowel syndrome.

Inflammatory diarrhea: Stools containing blood, pus (visible as thick white/yellow material), or mucus. Indicates intestinal inflammation, infection, or damage. Often associated with fever, abdominal pain, and urgency. Examples include inflammatory bowel disease (Crohn’s disease, ulcerative colitis), infectious colitis, ischemic colitis, and radiation colitis.

Characteristics that provide diagnostic clues:

• Blood in stool: Always concerning — suggests inflammation, infection, polyps, or cancer. Needs investigation.
• Mucus in stool: Common in IBS but also occurs in inflammatory conditions
• Greasy, floating, foul-smelling stools: Suggests fat malabsorption (steatorrhea)
• Nocturnal diarrhea: Waking from sleep to have diarrhea is a “red flag” — it suggests organic disease rather than functional. IBS very rarely causes nocturnal symptoms.
• Weight loss: Unintentional weight loss with diarrhea suggests malabsorption, chronic inflammation, or serious underlying disease
• Diarrhea relieved by fasting: Suggests osmotic cause — something you’re eating is causing it
• Diarrhea not relieved by fasting: Suggests secretory cause — the gut is secreting fluid regardless of intake
• Associated with specific foods: Suggests food intolerance (lactose, fructose) or allergy
• Relieved by defecation: Common in IBS
• Associated with stress: Common in IBS but doesn’t rule out other conditions

When chronic diarrhea requires urgent investigation:

• Persists more than four weeks without diagnosis
• Associated with unintentional weight loss (more than 5-10 pounds)
• Blood or pus in stool
• Nocturnal symptoms — waking to have diarrhea
• Fever
• Severe or worsening abdominal pain
• Signs of dehydration (dark urine, dizziness, rapid heart rate)
• Family history of inflammatory bowel disease, celiac disease, or colon cancer
• Recent antibiotic use (concern for C. difficile infection)
• New onset after age 50 (higher concern for cancer)
• Anemia or other concerning blood test abnormalities

Celiac Disease: The Hidden Cause

Celiac disease is an autoimmune condition where gluten (a protein found in wheat, barley, and rye) triggers an immune response that damages the small intestine. It affects approximately 1% of the population — that’s millions of people — but remarkably, the majority of cases remain undiagnosed. Many people with celiac disease are told they have IBS, food sensitivities, or just “a sensitive stomach” for years before getting the correct diagnosis.

Celiac disease is sometimes called “the great mimicker” because it can present with a wide variety of symptoms — or sometimes almost no symptoms at all. Some people have classic digestive symptoms; others present only with anemia or osteoporosis without any obvious GI complaints.

How celiac disease causes diarrhea:

In celiac disease, gluten triggers an autoimmune attack on the intestinal lining. The immune system mistakenly targets the villi — tiny finger-like projections that line the small intestine and are responsible for absorbing nutrients. Over time, this immune attack causes:

• Villous atrophy: The villi become flattened and damaged, dramatically reducing the surface area available for absorption. The small intestine normally has a surface area about the size of a tennis court due to its villi; in celiac disease, this surface area is significantly reduced.
• Malabsorption: Damaged villi can’t properly absorb nutrients, fats, and fluids. Unabsorbed fats cause steatorrhea (fatty diarrhea). Unabsorbed carbohydrates are fermented by bacteria, producing gas and osmotic effects.
• Osmotic diarrhea: Unabsorbed nutrients draw water into the intestine, increasing stool volume and liquidity.
• Increased intestinal permeability: The damaged intestinal barrier allows substances to pass through that shouldn’t — a phenomenon sometimes called “leaky gut.”
• Chronic inflammation: Ongoing immune activation in the gut wall perpetuates damage and symptoms.

Characteristics of celiac-related diarrhea:

• Chronic, often pale, bulky, foul-smelling stools
• Steatorrhea (fatty stools that may float and be difficult to flush) due to fat malabsorption
• Bloating and excessive, often foul-smelling gas
• Symptoms that may correlate with gluten intake (though this isn’t always obvious — people eating gluten regularly have constant exposure)
• May alternate with periods of constipation in some people
• Abdominal discomfort, cramping, or pain
• Nausea

Other symptoms often present with celiac disease:

• Fatigue: Often profound, due to nutrient malabsorption and chronic inflammation — many people describe being “bone-tired”
• Unintentional weight loss: Despite eating normally or even increased appetite
• Iron deficiency anemia: Often the presenting finding, even without obvious GI symptoms — iron is absorbed in the upper small intestine, which is damaged first
• Bone disease: Osteoporosis or osteopenia from calcium and vitamin D malabsorption — may present as bone pain, fractures with minimal trauma, or abnormal bone density screening
• Dermatitis herpetiformis: An intensely itchy, blistering skin rash, often on elbows, knees, buttocks, and scalp — this is actually celiac disease of the skin and is nearly 100% specific for celiac
• Mouth ulcers: Recurrent canker sores (aphthous ulcers)
• Joint pain: Arthralgia without obvious arthritis
• Neurological symptoms: Peripheral neuropathy (numbness/tingling), balance problems (ataxia), headaches — these can occur even without digestive symptoms
• Depression and anxiety: Common in celiac disease, may improve on gluten-free diet
• Brain fog: Difficulty concentrating, memory problems
• Elevated liver enzymes: Unexplained mild ALT elevation
• Dental enamel defects: Especially if celiac developed during childhood
• In children: Failure to thrive, delayed puberty, short stature, irritability

Importantly, many people with celiac disease — perhaps 30-40% — have minimal or no obvious digestive symptoms. They may present only with anemia, osteoporosis, infertility, or fatigue. This “silent” or “atypical” celiac disease is why screening should be considered broadly, not just in people with classic diarrhea.

Who should be tested for celiac disease:

• Anyone with chronic diarrhea without clear cause
• Unexplained iron deficiency anemia, especially if unresponsive to iron supplementation
• Unexplained osteoporosis or osteopenia, especially at a young age or in men
• First-degree relatives of people with celiac disease (10-15% will have it too)
• Type 1 diabetes (associated autoimmune condition — 5-10% have celiac)
• Autoimmune thyroid disease (Hashimoto’s, Graves’)
• Down syndrome, Turner syndrome, Williams syndrome (increased risk)
• Unexplained elevated liver enzymes
• Dermatitis herpetiformis (this essentially confirms celiac)
• Recurrent miscarriages or unexplained infertility
• IgA nephropathy
• Chronic fatigue without explanation
• Peripheral neuropathy without explanation

What to test:

Tissue transglutaminase IgA (tTG-IgA) is the primary screening test for celiac disease. It’s highly sensitive (95-98%) and specific (95-97%) when performed while the person is actively eating gluten. A positive tTG-IgA strongly suggests celiac disease.

Total IgA should be measured alongside tTG-IgA. About 2-3% of people with celiac disease have IgA deficiency (they don’t make enough IgA antibodies). In IgA deficiency, tTG-IgA can be falsely negative even when celiac disease is present. Checking total IgA identifies these people.

If IgA deficient, alternative tests should be used: tTG-IgG or deamidated gliadin peptide (DGP) IgG antibodies can detect celiac disease in IgA-deficient individuals.

Important: You must be eating gluten for celiac blood tests to be accurate. Antibody levels drop when gluten is removed from the diet. Going gluten-free before testing is a common reason for false-negative results. If you’ve already gone gluten-free, a “gluten challenge” (eating gluten for several weeks) may be needed before testing.

Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) includes two main conditions — Crohn’s disease and ulcerative colitis — both characterized by chronic inflammation of the digestive tract. Unlike IBS (irritable bowel syndrome), IBD involves actual visible damage and inflammation in the intestines. IBD affects over 3 million Americans and is a significant cause of chronic diarrhea, particularly bloody diarrhea.

IBD is an autoimmune-like condition where the immune system mistakenly attacks the digestive tract. The exact cause isn’t fully understood, but genetics, environment, and gut microbiome all play roles. IBD typically begins in young adulthood and follows a relapsing-remitting course — periods of active disease (flares) alternating with periods of remission.

Crohn’s disease:

Crohn’s disease can affect any part of the digestive tract from mouth to anus, though it most commonly affects the end of the small intestine (terminal ileum) and the beginning of the colon. Key features include:

• “Skip lesions”: Inflammation is patchy — areas of diseased intestine interspersed with normal areas
• Transmural inflammation: Inflammation extends through the entire thickness of the intestinal wall, not just the surface
• Complications: The deep inflammation can lead to strictures (narrowing), fistulas (abnormal connections between organs), and abscesses

Symptoms of Crohn’s disease include:

• Chronic diarrhea — often without visible blood (unlike ulcerative colitis)
• Abdominal pain, often in the right lower quadrant (where the terminal ileum is located)
• Unintentional weight loss — often significant, from malabsorption and decreased appetite
• Poor appetite
• Fatigue — often profound
• Fever during flares
• Mouth sores (aphthous ulcers)
• Perianal disease — fistulas, abscesses, skin tags around the anus (a distinguishing feature from UC)
• Nausea and vomiting if there’s obstruction
• Growth delay in children

Ulcerative colitis:

Ulcerative colitis affects only the colon (large intestine) and rectum. Key features include:

• Continuous inflammation: Unlike Crohn’s patchy pattern, UC inflammation is continuous, starting at the rectum and extending proximally
• Mucosal inflammation: Limited to the innermost lining (mucosa) — doesn’t go through the full wall thickness
• Always involves the rectum: The rectum is always affected, though the extent up the colon varies

Symptoms of ulcerative colitis include:

• Bloody diarrhea — blood and mucus in stool is characteristic and nearly universal
• Urgency — intense, sudden need to defecate
• Tenesmus — painful feeling of needing to pass stool even when the bowel is empty; feeling of incomplete evacuation
• Abdominal cramping, often relieved (at least partially) by bowel movements
• Frequent, small stools — sometimes 10-20 times daily during flares
• Nocturnal symptoms — waking from sleep to have bowel movements (this distinguishes organic disease from IBS)
• Fatigue
• Weight loss (usually less severe than in Crohn’s)

Extraintestinal manifestations of IBD:

Both Crohn’s and ulcerative colitis can cause significant symptoms outside the digestive tract — these “extraintestinal manifestations” affect up to 40% of people with IBD:

• Joint problems: Arthritis (especially affecting large joints like knees), arthralgia, ankylosing spondylitis
• Skin problems: Erythema nodosum (painful red nodules on shins), pyoderma gangrenosum (severe skin ulcers)
• Eye inflammation: Uveitis, episcleritis — red, painful eyes
• Liver and bile duct disease: Primary sclerosing cholangitis (especially with UC)
• Kidney stones: Especially in Crohn’s with ileal disease (due to fat malabsorption affecting oxalate)
• Anemia: From blood loss, chronic disease, and/or nutrient deficiencies
• Osteoporosis: From inflammation, malabsorption, and steroid use
• Blood clots: Increased risk of venous thromboembolism

What to test:

Blood tests cannot definitively diagnose IBD (that requires endoscopy with biopsies), but they provide valuable supporting evidence and help assess disease activity:

hs-CRP and ESR — inflammatory markers that are often elevated during active IBD. These help differentiate IBD (inflammatory) from IBS (functional). However, normal inflammatory markers don’t completely rule out IBD — some people have active disease with normal CRP.

Complete blood count — may show:

• Anemia — from blood loss (especially in UC) or chronic disease
• Elevated white blood cells during inflammation or infection
• Elevated platelets (thrombocytosis) — a marker of active inflammation
• Low iron-related indices

Albumin — may be low in active disease due to inflammation, poor nutrition, or protein loss through the inflamed, leaky gut.

Ferritin, iron, vitamin B12, folate, and vitamin D — often deficient in IBD due to malabsorption, blood loss, decreased intake, or inflammation. B12 deficiency particularly suggests ileal Crohn’s (B12 is absorbed in the terminal ileum).

Stool calprotectin (not a blood test) is highly useful for IBD — it detects intestinal inflammation specifically and helps distinguish IBD from IBS. Elevated calprotectin warrants colonoscopy.

Hyperthyroidism: The Metabolic Accelerator

An overactive thyroid (hyperthyroidism) speeds up virtually every system in the body, including the digestive tract. While diarrhea may not be the first symptom that comes to mind when thinking about thyroid problems, increased stool frequency and loose stools are common manifestations of hyperthyroidism that are often overlooked.

How hyperthyroidism causes diarrhea:

Excess thyroid hormone affects the gut through several mechanisms:

• Increased gut motility: Thyroid hormones stimulate the muscles of the intestinal wall to contract more frequently and forcefully. Food and waste move through the digestive tract faster than normal, reducing the time available for water absorption. The result is looser, more frequent stools.
• Shortened transit time: The entire journey from mouth to colon is accelerated. Normal transit time through the gut is 24-72 hours; in hyperthyroidism, it can be significantly reduced.
• Increased secretion: The gut may secrete more fluid into the intestinal lumen.
• Malabsorption: Rapid transit can impair nutrient absorption because food doesn’t spend enough time in contact with the absorptive surface.
• Increased metabolism: The overall metabolic overdrive affects gut function along with everything else.

Characteristics of hyperthyroid-related diarrhea:

• Increased stool frequency — someone who normally goes once daily may find themselves going three, four, or more times
• Loose stools rather than well-formed — not necessarily watery, but definitely less solid than normal
• Urgency — feeling the need to go quickly when the urge arises
• Symptoms that developed gradually as thyroid function became progressively elevated
• May not be the primary complaint — weight loss, anxiety, palpitations often more prominent and distressing
• Typically not bloody (bloody stools suggest a different diagnosis)

Other symptoms typically present with hyperthyroidism:

Diarrhea from hyperthyroidism rarely occurs in isolation — it’s usually accompanied by other symptoms of metabolic overdrive:

• Unintentional weight loss despite increased appetite and eating — one of the most common symptoms
• Rapid or irregular heartbeat, palpitations — can feel like heart is racing or skipping beats
• Anxiety, nervousness, irritability — feeling “wired” or on edge
• Tremor — fine shaking of the hands, most visible when holding them out straight
• Heat intolerance and increased sweating — feeling hot when others are comfortable
• Fatigue and muscle weakness — despite the “revved up” feeling, people often feel exhausted
• Difficulty sleeping — insomnia, difficulty staying asleep
• Thinning skin and fine, brittle hair
• Menstrual changes in women — lighter, less frequent periods
• In Graves’ disease specifically: Bulging eyes (exophthalmos), eye irritation, double vision

The combination of diarrhea with weight loss, anxiety, rapid heart rate, and heat intolerance should strongly prompt thyroid testing. These symptoms together are highly suggestive of hyperthyroidism.

What to test:

TSH (Thyroid-Stimulating Hormone) is the primary screening test. In hyperthyroidism, TSH is suppressed (very low, often near zero) because the pituitary gland reduces its stimulation when thyroid hormone levels are already too high. The pituitary is saying “stop making more!”

Free T4 — elevated in most cases of hyperthyroidism. This is the main hormone produced by the thyroid.

Free T3 — may be elevated even more prominently than T4, and some people have “T3 toxicosis” where T3 is elevated while T4 is normal or only slightly elevated.

TSH receptor antibodies (TRAb) — positive in Graves’ disease, the most common cause of hyperthyroidism. These antibodies stimulate the thyroid to overproduce hormone.

Diabetes and Diarrhea

Chronic diarrhea is a common but underrecognized complication of diabetes, affecting up to 22% of people with long-standing diabetes. Multiple mechanisms can be involved.

How diabetes causes diarrhea:

Diabetic autonomic neuropathy: Diabetes can damage the nerves controlling the GI tract, leading to:

• Altered gut motility — may cause rapid transit and diarrhea or slow transit and constipation (or both alternating)
• Impaired sphincter function
• Abnormal secretion and absorption

Small intestinal bacterial overgrowth (SIBO): Diabetic gut dysmotility can lead to bacterial overgrowth in the small intestine, causing diarrhea, bloating, and malabsorption.

Exocrine pancreatic insufficiency: The pancreas may not produce enough digestive enzymes, leading to fat malabsorption and steatorrhea.

Celiac disease: Type 1 diabetes is associated with increased risk of celiac disease (both are autoimmune).

Metformin: This common diabetes medication frequently causes diarrhea as a side effect, especially when first started or at higher doses.

Characteristics of diabetic diarrhea:

• Often watery, explosive diarrhea
• May be nocturnal (classic feature)
• Can alternate with constipation
• Often associated with fecal incontinence
• Usually occurs in people with long-standing diabetes and other complications

What to test:

Fasting glucose and HbA1c — to assess diabetes control. Poor control is associated with more complications.

Vitamin B12 — metformin reduces B12 absorption.

Celiac serology if type 1 diabetes — tTG-IgA.

Microscopic Colitis

Microscopic colitis is a frequently underdiagnosed cause of chronic watery diarrhea, particularly in older adults. The colon appears normal on colonoscopy, but microscopic examination of biopsies reveals characteristic inflammation.

Types of microscopic colitis:

• Collagenous colitis: Thickened collagen band under the intestinal lining
• Lymphocytic colitis: Increased lymphocytes in the intestinal lining

Characteristics:

• Chronic, watery, non-bloody diarrhea — often 4-9 watery stools daily
• Nocturnal diarrhea common
• Abdominal cramping
• Urgency and fecal incontinence
• Often affects women over 50
• Associated with autoimmune diseases, celiac disease, and certain medications (NSAIDs, PPIs, SSRIs)

What to test:

Blood tests are usually normal or show only mild nonspecific abnormalities. Diagnosis requires colonoscopy with biopsies.

However, blood tests can rule out other conditions and check for associated conditions:

• tTG-IgA — celiac disease is associated with microscopic colitis
• TSH — thyroid disease association
• Inflammatory markers — usually normal (helpful to distinguish from IBD)

Food Intolerances

Food intolerances — difficulty digesting certain foods — are common causes of chronic diarrhea. Unlike food allergies (immune-mediated), intolerances are usually caused by enzyme deficiencies or sensitivity to food components.

Lactose intolerance:

The most common food intolerance worldwide, affecting 68% of the world’s population to some degree. Lactase, the enzyme that digests lactose (milk sugar), decreases after childhood in most people.

Symptoms occur 30 minutes to 2 hours after consuming dairy:

• Diarrhea
• Bloating and gas
• Abdominal cramps
• Nausea

Severity depends on the amount consumed and individual tolerance level. Many people can tolerate small amounts but have symptoms with larger quantities.

Fructose malabsorption:

Difficulty absorbing fructose (fruit sugar), found in fruits, honey, and high-fructose corn syrup. When fructose isn’t absorbed, it’s fermented by gut bacteria, causing gas, bloating, and diarrhea.

Sugar alcohols:

Sorbitol, mannitol, xylitol, and other sugar alcohols (found in sugar-free products) are poorly absorbed and can cause osmotic diarrhea when consumed in excess.

FODMAPs:

Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols — a group of poorly absorbed short-chain carbohydrates that can cause digestive symptoms in susceptible people, particularly those with IBS.

What to test:

Food intolerances are typically diagnosed through elimination diets and symptom observation rather than blood tests. However:

Celiac serology should be done to rule out celiac disease, which can mimic food intolerance.

Hydrogen breath tests (not blood tests) can diagnose lactose and fructose malabsorption.

Bile Acid Malabsorption

Bile acid malabsorption (BAM), also called bile acid diarrhea, is an underdiagnosed cause of chronic diarrhea. Normally, bile acids secreted to help digest fat are reabsorbed in the terminal ileum. When reabsorption fails, excess bile acids reach the colon and cause secretory diarrhea.

Causes of bile acid malabsorption:

• Type 1: Ileal disease or resection — Crohn’s disease, surgical removal of ileum
• Type 2: Primary/idiopathic — the most common type, no obvious cause
• Type 3: Secondary to other GI conditions — celiac disease, SIBO, post-cholecystectomy, radiation

Characteristics:

• Watery diarrhea, often urgent
• May be worse after fatty meals (which stimulate bile release)
• Often occurs post-cholecystectomy (gallbladder removal)
• Bloating and cramping
• Symptoms may be worse in the morning

What to test:

SeHCAT scan (not widely available) is the gold standard for diagnosis. Blood tests for 7α-hydroxy-4-cholesten-3-one (C4) can indicate bile acid synthesis rate but aren’t widely available.

Often, a therapeutic trial of bile acid sequestrants (cholestyramine) is used — dramatic improvement supports the diagnosis.

Blood tests to check for underlying causes:

• hs-CRP — for Crohn’s disease
• tTG-IgA — for celiac disease
• Vitamin B12 — ileal disease can cause B12 deficiency

Infections and Post-Infectious Causes

Chronic infections:

While most infectious diarrhea is acute, some infections can cause chronic symptoms:

• Giardia: A parasite that can cause prolonged diarrhea, especially in travelers
• Cryptosporidium: Can cause chronic diarrhea, especially in immunocompromised individuals
• C. difficile: Can become chronic or recurrent, especially after antibiotic use
• Small intestinal bacterial overgrowth (SIBO): Overgrowth of bacteria in the small intestine causing diarrhea, bloating, and malabsorption

Post-infectious IBS:

After an acute infectious gastroenteritis episode, some people develop chronic IBS-like symptoms including diarrhea. This “post-infectious IBS” can persist for months or years after the original infection has cleared.

What to test:

Stool tests rather than blood tests are primary for diagnosing GI infections. However, blood tests can assess impact:

• CBC — eosinophilia may suggest parasitic infection
• Nutritional markers — chronic infection can cause deficiencies
• hs-CRP — may be elevated with infection

Irritable Bowel Syndrome (IBS)

IBS is a functional gastrointestinal disorder — the gut doesn’t function normally, but there’s no visible structural damage, inflammation, or abnormality on testing. It’s extremely common, affecting 10-15% of adults worldwide, making it one of the most frequent reasons people see gastroenterologists.

Despite being “functional” (not caused by visible disease), IBS is a real condition that causes real symptoms and significantly impacts quality of life. It’s not “all in your head,” though stress and psychological factors can influence symptoms. The current understanding is that IBS involves abnormalities in gut-brain communication, gut motility, visceral sensitivity (the gut is hypersensitive to normal sensations), gut microbiome, and possibly low-grade inflammation not detectable by standard tests.

IBS-D (diarrhea-predominant):

IBS comes in different subtypes based on predominant symptoms. IBS-D is characterized by:

• Recurrent abdominal pain associated with changes in stool frequency or form — at least one day per week on average for the past three months
• Diarrhea — loose or watery stools on more than 25% of bowel movements
• Urgency — needing to get to a bathroom quickly
• Symptoms often related to meals — eating triggers symptoms within 30-90 minutes
• Symptoms often related to stress — worse during stressful periods
• Symptoms often improve with defecation — though incomplete relief is common
• Bloating and gas are extremely common
• Symptoms may fluctuate — good days and bad days

Red flags that suggest NOT IBS:

The following features suggest organic disease rather than IBS and warrant investigation:

• Nocturnal symptoms — waking from sleep to have diarrhea is unusual in IBS
• Unintentional weight loss
• Blood in stool (other than from hemorrhoids with straining)
• Fever
• Anemia
• Elevated inflammatory markers
• New onset after age 50
• Family history of colon cancer, IBD, or celiac disease
• Progressive worsening of symptoms

If red flags are absent and symptoms fit the pattern, IBS can be diagnosed clinically without extensive testing. However, most guidelines recommend basic blood tests to rule out common organic causes.

What to test:

IBS is a diagnosis of exclusion — meaning blood tests are done to rule out other conditions rather than to positively diagnose IBS:

• CBC — rule out anemia
• tTG-IgA — rule out celiac disease (celiac and IBS symptoms overlap significantly)
• hs-CRP and/or stool calprotectin — rule out inflammatory bowel disease
• TSH — rule out thyroid dysfunction

If these tests are normal and symptoms fit the clinical pattern without red flags, IBS can be diagnosed based on Rome IV criteria without further invasive testing.

Nutritional Deficiencies from Chronic Diarrhea

Chronic diarrhea — regardless of its underlying cause — can lead to nutritional deficiencies through malabsorption and direct losses in stool. Testing for these deficiencies serves two purposes: identifying health consequences that need to be addressed, and providing clues about the underlying cause of the diarrhea.

The pattern of deficiencies often points toward the location and mechanism of the problem. For example, B12 deficiency suggests terminal ileal disease, while multiple fat-soluble vitamin deficiencies suggest widespread small bowel malabsorption.

Common deficiencies and what they suggest:

Iron deficiency: The most common nutritional deficiency worldwide. In the context of chronic diarrhea, it may result from blood loss (common in IBD, especially ulcerative colitis), malabsorption (iron is absorbed in the duodenum and upper jejunum, which are affected in celiac disease), or chronic inflammation (which sequesters iron). May present as anemia, fatigue, weakness, or brittle nails.

Vitamin B12 deficiency: B12 is specifically absorbed in the terminal ileum, so B12 deficiency strongly suggests disease affecting that area — particularly Crohn’s disease affecting the ileum, surgical removal of the ileum, or small intestinal bacterial overgrowth (bacteria consume B12 before it can be absorbed). B12 deficiency causes fatigue, neurological symptoms (numbness, tingling, balance problems), and macrocytic anemia.

Folate deficiency: Folate is absorbed throughout the small intestine, so deficiency suggests more widespread small bowel disease. Common in celiac disease. Causes anemia and, in pregnancy, risk of neural tube defects.

Vitamin D deficiency: As a fat-soluble vitamin, vitamin D absorption requires normal fat digestion and absorption. Deficiency is common in any condition causing fat malabsorption — celiac disease, chronic pancreatitis, bile acid deficiency. Causes bone disease (osteomalacia, osteoporosis), muscle weakness, and potentially fatigue.

Vitamin A, E, K deficiencies: Other fat-soluble vitamins also affected in fat malabsorption. Vitamin A deficiency affects vision and skin. Vitamin E deficiency causes neurological problems. Vitamin K deficiency causes bleeding problems.

Zinc deficiency: Common in chronic diarrhea because zinc is lost in stool and absorption is impaired. Zinc deficiency impairs wound healing, immune function, taste, and smell. Can perpetuate diarrhea (zinc is needed for intestinal epithelial integrity).

Magnesium deficiency: Can be depleted through ongoing losses in diarrhea. Causes muscle cramps, weakness, and potentially heart rhythm disturbances.

Protein-calorie malnutrition: Severe or prolonged malabsorption can cause significant weight loss and protein deficiency, reflected in low albumin.

What to test:

• CBC — for anemia. Microcytic anemia (low MCV) suggests iron deficiency; macrocytic anemia (high MCV) suggests B12 or folate deficiency.
• Ferritin, iron, TIBC — comprehensive iron status
• Vitamin B12
• Folate
• Vitamin D
• Magnesium
• Albumin — marker of protein status and overall nutritional health

The pattern of deficiencies provides diagnostic clues: isolated B12 deficiency suggests terminal ileum problem specifically; iron deficiency with normal B12 suggests upper GI issue or blood loss; multiple fat-soluble vitamin deficiencies suggest fat malabsorption; widespread deficiencies suggest severe small bowel disease.

The Testing Strategy for Chronic Diarrhea

A logical approach to blood testing for chronic diarrhea:

First-line tests for everyone with chronic diarrhea:

Celiac screening:

• tTG-IgA
• Total IgA

Thyroid function:

• TSH

Inflammatory markers:

• hs-CRP

Blood count and nutrition:

• CBC
• Ferritin
• Vitamin B12
• Vitamin D
• Folate
• Albumin

Metabolic:

• Fasting glucose or HbA1c
• Creatinine, sodium, potassium — electrolytes can be depleted

Additional tests based on findings:

• If thyroid abnormality: complete thyroid panel (Free T4, Free T3)
• If inflammatory markers elevated: further IBD workup including colonoscopy
• If B12 deficient: evaluate for ileal disease, SIBO, pernicious anemia
• If multiple deficiencies: malabsorption workup

What to Do With the Results

If celiac disease is found:

Positive serology should be confirmed with small intestinal biopsy before starting treatment. Treatment is strict, lifelong gluten-free diet. Most people see significant improvement in diarrhea within weeks of removing gluten.

If hyperthyroidism is found:

Treatment depends on the cause but may include antithyroid medications, radioactive iodine, or surgery. Diarrhea typically resolves as thyroid levels normalize.

If inflammatory markers are elevated:

This warrants further investigation for IBD or other inflammatory conditions. Colonoscopy with biopsies is usually needed for definitive diagnosis.

If nutritional deficiencies are found:

Replace the deficient nutrients while investigating the cause. Isolated iron deficiency prompts looking for blood loss. B12 deficiency suggests ileal problems. Multiple deficiencies suggest significant malabsorption.

If diabetes is found or poorly controlled:

Optimize glucose control. Consider whether metformin is contributing. Evaluate for diabetic complications affecting the gut.

When Tests Are Normal

Normal blood tests don’t mean nothing is wrong — they mean the conditions detectable by standard blood tests aren’t present. Blood tests are just one piece of the diagnostic puzzle. If blood tests are normal but diarrhea persists, consider these possibilities:

• IBS-D (Irritable Bowel Syndrome, diarrhea-predominant): A real condition causing real symptoms — but by definition, blood tests and imaging are normal. IBS affects 10-15% of the population and is diagnosed based on clinical criteria. Treatment focuses on dietary modifications (low-FODMAP diet often helps), stress management, and medications that target symptoms.
• Food intolerances: Lactose intolerance, fructose malabsorption, and sensitivity to FODMAPs don’t show up on blood tests. Diagnosis is made through elimination diets (remove suspected foods, see if symptoms improve) or breath tests for lactose and fructose.
• Bile acid malabsorption: This common cause of chronic watery diarrhea is not reliably detected by standard blood tests. The gold standard is SeHCAT scan (not widely available), but often a therapeutic trial of bile acid sequestrants (like cholestyramine) is used — dramatic improvement supports the diagnosis.
• Microscopic colitis: Blood tests are usually completely normal in this condition. The colon looks normal on colonoscopy too — diagnosis requires taking biopsies and examining them under a microscope. If watery diarrhea persists with normal blood tests, colonoscopy with biopsies should be considered.
• Medication effects: Many medications cause diarrhea as a side effect — metformin, antibiotics, NSAIDs, proton pump inhibitors, magnesium supplements, artificial sweeteners, herbal supplements. Review all medications, prescription and over-the-counter, with your healthcare provider.
• Dietary factors: Excessive caffeine, alcohol, artificial sweeteners (especially sugar alcohols like sorbitol, mannitol, xylitol), and very high-fiber intake can all cause diarrhea. A food diary can help identify patterns.
• Functional diarrhea: Chronic painless diarrhea that doesn’t meet full IBS criteria — another functional bowel disorder with normal testing.
• SIBO (Small Intestinal Bacterial Overgrowth): Overgrowth of bacteria in the small intestine causing diarrhea, bloating, and malabsorption. Diagnosed with breath testing, not blood tests.
• Stress and anxiety: The gut-brain connection is real. Chronic stress can genuinely cause digestive symptoms including diarrhea, even without underlying disease.

Normal blood tests are actually useful information — they’ve ruled out celiac disease, significant inflammation, thyroid dysfunction, diabetes, and nutritional deficiencies. This narrows the focus and points toward conditions that require different diagnostic approaches.

The Bottom Line

Chronic diarrhea is your body signaling that something in your digestive system needs attention. While acute diarrhea — from a stomach bug or food poisoning — usually resolves on its own, diarrhea lasting more than four weeks deserves investigation. It’s not something to simply accept or manage with over-the-counter medications indefinitely.

Blood tests can identify many important causes of chronic diarrhea:

• Celiac disease — affecting 1% of the population, often undiagnosed, easily screened with tTG-IgA
• Hyperthyroidism — speeds up gut motility along with everything else, detected with TSH
• Inflammatory bowel disease — causes bloody diarrhea with systemic inflammation, suggested by elevated inflammatory markers
• Diabetes complications — diabetic gut neuropathy and associated conditions
• Nutritional deficiencies — both a consequence of and clue to the cause of malabsorption

Finding the cause matters because treatment depends on it. A strict gluten-free diet resolves celiac disease — but only if you know to do it. Thyroid treatment normalizes gut motility in hyperthyroidism. IBD requires specific anti-inflammatory therapies. Treating the wrong diagnosis or no diagnosis at all leaves you suffering unnecessarily.

Even when blood tests are normal, they’ve provided valuable information by ruling out important conditions. Normal celiac serology, thyroid function, and inflammatory markers point the investigation toward other causes — IBS, food intolerances, bile acid malabsorption, microscopic colitis — that require different approaches to diagnose.

You don’t have to accept chronic diarrhea as your normal. You don’t have to memorize the location of every bathroom or plan your life around unpredictable bowel habits. Identifying the cause is the first step toward treatment — and toward getting your digestive system, and your life, back to normal.

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Key Takeaways

• Chronic diarrhea (lasting 4+ weeks) usually has an identifiable cause — investigation is warranted
• Celiac disease affects 1% of the population and is often undiagnosed — everyone with chronic diarrhea should be screened
• Hyperthyroidism accelerates gut motility — thyroid testing is part of diarrhea workup
• Inflammatory bowel disease causes bloody diarrhea with systemic inflammation — inflammatory markers help identify it
• Diabetes can cause diarrhea through multiple mechanisms — diabetic gut neuropathy, SIBO, metformin, and associated celiac disease
• Nutritional deficiencies both result from and provide clues about the cause — check iron, B12, folate, vitamin D
• Normal blood tests rule out many conditions — but consider IBS, food intolerances, bile acid malabsorption, and microscopic colitis
• The pattern of diarrhea provides diagnostic clues — bloody vs. watery, nocturnal vs. daytime, related to eating or not
• Treatment depends on cause — identifying the underlying condition is essential for effective treatment