When Diarrhea Is Not an Infection

Acute diarrhoea lasting a few days is usually infectious and self-limiting. But when loose, watery, or urgent stools persist for four weeks or more without an identifiable pathogen, the investigation must shift to non-infectious causes. Chronic diarrhoea affects approximately 5 percent of the population in Western countries, and many individuals suffer for months or years before receiving an accurate diagnosis. The reason for this delay is that non-infectious chronic diarrhoea has a broad differential diagnosis, and several of the most common causes are poorly recognised even among general practitioners.

Bile Acid Malabsorption

Bile acid malabsorption (BAM) is arguably the most under-diagnosed cause of chronic diarrhoea. It affects an estimated one in three patients labelled with IBS-D, yet it is rarely tested for in primary care. Normally, 95 percent of bile acids are reabsorbed in the terminal ileum and recycled. When this reabsorption fails, excess bile acids enter the colon, where they stimulate water and electrolyte secretion and accelerate motility.

BAM causes watery, urgent diarrhoea that is often worst in the morning or after fatty meals. It has three types:

  • Type 1 — caused by ileal disease or resection (Crohn's disease, surgical removal of the terminal ileum)
  • Type 2 — idiopathic (primary), where the feedback mechanism controlling bile production is defective. This is the most common type
  • Type 3 — secondary to cholecystectomy, coeliac disease, SIBO, or radiation enteritis

Diagnosis is via SeHCAT scan (where available) or a therapeutic trial of cholestyramine. Response rates to bile acid sequestrants are 60 to 80 percent, making BAM one of the most treatable causes of chronic diarrhoea.

Microscopic Colitis

Microscopic colitis is a chronic inflammatory condition of the colon that causes persistent watery diarrhoea but appears completely normal on colonoscopy to the naked eye. Inflammation is only visible under a microscope, hence the name. It comes in two forms: collagenous colitis and lymphocytic colitis.

Microscopic colitis is more common in women over 50 and is associated with autoimmune conditions, NSAID use, and proton pump inhibitor use. The hallmark is profuse watery diarrhoea (often 5 to 10 watery stools per day) without bleeding. Because the colon looks normal on endoscopy, the diagnosis is missed unless biopsies are taken from a macroscopically normal-appearing colon.

If you have chronic watery diarrhoea and a colonoscopy was reported as normal, ask whether biopsies were taken. A normal-looking colonoscopy without biopsies cannot exclude microscopic colitis. This is one of the most commonly missed diagnoses in gastroenterology.

Food Intolerances

Carbohydrate malabsorption is a common cause of chronic diarrhoea that often goes undiagnosed:

  • Lactose intolerance — affects 68 percent of the global population. Undigested lactose draws water into the gut and is fermented by bacteria, causing diarrhoea, gas, and cramping
  • Fructose malabsorption — the intestine has limited capacity to absorb fructose; when intake exceeds this capacity, diarrhoea results. Modern diets high in high-fructose corn syrup, fruit juices, and honey frequently overwhelm fructose absorption
  • Sorbitol and other sugar alcohols — found in sugar-free products, these are poorly absorbed and have an osmotic laxative effect
  • FODMAP intolerance — a broader category of fermentable carbohydrates that cause diarrhoea in sensitive individuals

Hydrogen breath tests can diagnose lactose and fructose malabsorption, and a low-FODMAP elimination diet can identify broader carbohydrate sensitivities.

Coeliac Disease

Coeliac disease causes chronic diarrhoea through autoimmune destruction of the small intestinal villi, reducing absorptive surface area. It affects approximately 1 percent of the population but is estimated to be undiagnosed in up to 80 percent of affected individuals. Screening with a tTG-IgA blood test is simple and should be performed in all patients with unexplained chronic diarrhoea. Importantly, gluten must be actively consumed during testing for results to be reliable.

Small Intestinal Bacterial Overgrowth

SIBO causes chronic diarrhoea through premature fermentation of carbohydrates in the small intestine, bile acid deconjugation leading to fat malabsorption, and direct inflammation of the small intestinal lining. Hydrogen-dominant SIBO typically presents with diarrhoea, while methane-dominant overgrowth presents with constipation. Hydrogen sulphide SIBO may present with either pattern plus characteristic sulphurous gas.

Less Common But Important Causes

  • Pancreatic insufficiency — produces steatorrhoea (fatty diarrhoea) with pale, oily stools. Diagnosed by faecal elastase
  • Hyperthyroidism — excess thyroid hormone directly accelerates gut motility
  • Carcinoid tumour — rare neuroendocrine tumours that secrete serotonin and other vasoactive substances causing secretory diarrhoea
  • Addison's disease — adrenal insufficiency can cause chronic diarrhoea

A Diagnostic Approach

If you have chronic diarrhoea without an identified cause, a systematic investigation should include coeliac serology, thyroid function, faecal calprotectin, faecal elastase, bile acid testing, hydrogen breath tests, and colonoscopy with biopsies even if the mucosa appears normal. GutIQ can help you document your symptom patterns, stool characteristics, and dietary associations to present to your gastroenterologist, ensuring that the right tests are ordered based on your specific presentation.