How Long Can Poop Stay in Your Body Before It Impacts Your Health?

• Research suggests that the amount of time stool spends in your body may affect your overall health.
• This may be due to changes in gut microbiomes associated with how quickly or slowly stool moves through the body.
• An expert explains long-term health issues associated with slow digestion, chronic constipation, and chronic diarrhea.

The amount of time it takes for stool to move through your body may impact your health in more ways than you may think.

A 2023 study showed that there may be distinct differences in gut microbiomes depending on whether your stool is fast or slow.

This study also looked at previous research on gut transit time. All of the research had the same goal of estimating how long food stays in a person’s colon.

The longer it stays, the more time bacteria have to ferment the contents, regulate acidity in the gut, and produce metabolites that can influence the body’s health.

The study found that people with faster gut transit times had drastically different microbiomes than those with slower transit times.

One approach to estimating the gut transit time was the Bristol Stool Scale. This is a visual tool that classifies stool by consistency. For example, hard, rock-like pellets typically mean a long transit time. Watery, mushy stool often indicates a short transit time.

Transit time can also influence how your body responds to probiotics, as well as supplements and medications that interact with the gut.

“The gut is far more than a digestive organ — it is a finely tuned ecosystem whose balance underpins everything from immune function and metabolic health to neurological well-being and cancer risk,” said Ketan Thanki, MD, board certified colorectal surgeon who specializes in benign and malignant disease of the colon, rectum, and anus with the MemorialCare Todd Cancer Institute at Long Beach Medical Center in Long Beach, CA.

Healthline spoke with Thanki to learn more about how poop transit time can impact health.

This interview has been lightly edited for length and clarity.

Thanki: Gut transit time is a major determinant of microbiome composition, diversity, and metabolism.

Slower colonic transit time is consistently associated with a shift away from beneficial sugar fermentation, which produces health-promoting short-chain fatty acids (SCFAs) and toward protein fermentation that generates potentially harmful byproducts like ammonia and phenols.

The relationship works both ways: transit time shapes which microbial communities thrive, but microbiota and their metabolites — including SCFAs and secondary bile acids — directly influence gut motility.

Thanki: When transit slows, fermentable carbohydrates become depleted before stool reaches the distal colon, and bacteria switch from fermenting carbohydrates into healthful short-chain fatty acids to fermenting proteins instead (proteolysis).

This produces metabolites — ammonia, hydrogen sulfide, phenols, indoles, and branched-chain fatty acids — that are directly toxic to colonocytes, damage colonocyte DNA, cause cancer-causing mutations, and promote a leaky gut lining, thereby promoting systemic inflammation.

Meanwhile, increased methane production further slows the gut, and increased estrogens in the blood can increase the risk of malignancies like breast cancer and dysregulate levels of other hormones.

SCFA depletion affects systemic metabolism. SCFAs are not just local (colonocyte) fuel. They also signal to the liver to regulate glucose production, and influence adipose tissue metabolism, insulin sensitivity, and secretion of appetite hormones (GLP-1, PYY).

When prolonged transit time reduces SCFA production, these regulatory signals are diminished. This is particularly relevant in diabetes and obesity, where gastroparesis and altered transit compound glycemic control problems and energy dysregulation.

Lastly, gut bacteria convert choline and carnitine from meat and eggs into trimethylamine (TMA), which the liver converts to TMAO, a metabolite linked to cardiovascular disease. The paper notes the transit-TMAO link hasn’t been fully characterized yet, but it’s a plausible pathway to worsened heart disease.

Thanki: Colorectal cancer is one of the most well-established and serious associations with chronic constipation.

Slow transit promotes the accumulation of secondary bile acids that are directly genotoxic and cytotoxic to colonocytes.

Combined with the shift toward proteolytic fermentation generating ammonia, phenols, and hydrogen sulfide — all of which damage the mucosal barrier and colonocyte DNA — and the depletion of protective butyrate (a SCFA), the colonic environment becomes progressively more hostile over time.

The distal colon, where proteolysis dominates and transit is slowest, is also where most colorectal tumors arise.

Thanki: Eat lots of fiber (I suggest aiming for 35 g a day), drink lots of water (64 to 80 ounces a day), and minimize red and processed meats (3 portions of red meat a week and only eat processed meats rarely or sparingly).

Try to get your fiber from varied sources like vegetables, seeds, and whole grains, and don’t hesitate to take a fiber supplement like psyllium husk.

Probiotic foods like yogurt, kefir, kombucha, and sauerkraut can help restore gut flora, especially sugar-fermenting bacteria.

Finally, exercise! Even 20 to 30 minutes of walking a day will stimulate your gut motility.

Thanki: Think beyond your diet — while food and water intake are major contributors, constipation is multifactorial.

Move your body regularly: Even a daily 20 to 30-minute walk can stimulate bowel activity.

Don’t hold in your bowel movements: Ignoring the urge to defecate retrains your bowel to live with constipation.

Try lifestyle modifications to help with stress, poor sleep, and reduce medications that might slow things down. These can all contribute to nervous system and hormonal dysregulation that, in turn, affects gut motility.

If constipation persists for more than a few weeks despite lifestyle modification, there’s likely something more going on. Listen to your body and get it checked out.

Thanki: Chronic diarrhea accelerates gut transit to the point where adequate nutrient absorption and microbial fermentation cannot occur, leading to a cascade of long-term systemic consequences, including:

The persistently compromised gut barrier allows bacterial products to enter systemic circulation, driving low-grade inflammation linked to autoimmune conditions, while the depleted SCFA production starves colonocytes and further destabilizes the mucosal lining.