When a lab receives your stool sample, what they test for depends on why your doctor ordered it. A stool sample can reveal bacterial and viral infections, parasites, signs of inflammation, hidden blood, digestive problems, and even early markers of colon cancer. Most people giving a sample are being tested for one or two of these things, not all of them at once.
Bacterial Infections
A standard stool culture screens for the bacteria most likely to cause food poisoning and infectious diarrhea: Salmonella, Shigella, Campylobacter, and Yersinia. The lab places a small amount of your stool on growth plates designed to encourage these specific organisms while suppressing the billions of normal gut bacteria that would otherwise overwhelm the sample.
If your doctor suspects a hospital-acquired or antibiotic-related infection, they’ll specifically order testing for C. difficile, a bacterium that can take over the gut after antibiotic use. C. diff testing typically uses a two-step process. A rapid antigen test (results in under an hour) checks whether the organism is present, and then a more precise molecular test confirms whether it’s actually producing the toxins that cause illness. This distinction matters because some people carry C. diff without being sick, and a positive molecular test alone can lead to unnecessary treatment.
Viruses
Newer multiplex PCR panels can scan a single stool sample for dozens of pathogens at once, including viruses that traditional cultures would miss entirely. These panels typically check for norovirus, rotavirus, adenovirus, astrovirus, and sapovirus. PCR testing works by detecting tiny fragments of viral genetic material, so it can identify infections even when the amount of virus in the sample is small. Results usually come back the same day.
Parasites
An ova and parasite test (often written as “O&P” on lab orders) looks for parasitic organisms and their eggs under a microscope. The most common parasites detected in the U.S. are Giardia, Cryptosporidium, and Entamoeba histolytica (which causes amebiasis). Your doctor might order this test if you’ve had prolonged diarrhea, recently traveled internationally, or drank untreated water. Because parasites shed intermittently, you may be asked to collect samples on two or three separate days to improve the chances of catching them.
Hidden Blood
Fecal occult blood tests look for blood you can’t see with the naked eye. Even tiny amounts of bleeding from a polyp or tumor higher up in the colon can leave traces in stool, making this one of the primary screening tools for colorectal cancer.
There are two main versions. The older guaiac-based test (gFOBT) uses a chemical reaction to detect blood and catches about 50% to 70% of colorectal cancers. The newer fecal immunochemical test (FIT) uses antibodies that specifically target human blood proteins, giving it better sensitivity of around 70% to 86% with fewer false positives. FIT has largely replaced the guaiac test in screening programs because of this improved accuracy. A large meta-analysis of 31 studies across China, Europe, and the U.S. confirmed FIT’s advantage: 86% sensitivity compared to 68% for gFOBT.
One thing worth knowing: proton pump inhibitors (common heartburn medications) can increase the odds of a false-positive FIT result, as can hemorrhoids and anal fissures. If you’re taking a PPI, your doctor may want to account for that when interpreting the results.
Inflammation Markers
When doctors need to figure out whether your gut symptoms come from something structural like Crohn’s disease or ulcerative colitis versus something functional like irritable bowel syndrome, they often order a calprotectin test. Calprotectin is a protein released by white blood cells when there’s active inflammation in the intestinal lining.
Normal calprotectin is below 50 micrograms per gram of stool. At that cutoff, the test correctly identifies inflammatory bowel disease (IBD) about 89% of the time and correctly rules it out about 81% of the time. At 100 micrograms per gram (twice the upper limit of normal), accuracy improves further, with 98% sensitivity and 91% specificity. A calprotectin level below 60 has essentially a 100% negative predictive value for active Crohn’s disease, meaning if your number is that low, active Crohn’s is extremely unlikely. This single test can save many patients from needing a colonoscopy just to distinguish IBD from IBS.
Lactoferrin is another inflammation marker sometimes tested alongside calprotectin, with normal levels below 7.25 micrograms per gram. Both are elevated in active IBD, infections, and certain intestinal cancers.
Digestive Function
Stool tests can also reveal how well your pancreas and digestive system are breaking down food. Two tests are commonly used here.
Fecal elastase measures an enzyme your pancreas produces to digest protein. Levels above 500 micrograms per gram indicate normal pancreatic function. Below 200 suggests exocrine pancreatic insufficiency, meaning your pancreas isn’t producing enough digestive enzymes. The zone between 200 and 500 is a gray area where symptoms and additional testing help clarify the picture. This test is especially useful for people with chronic diarrhea, unexplained weight loss, or conditions like chronic pancreatitis or cystic fibrosis.
Fecal fat testing checks whether your body is properly absorbing dietary fat. For this test, you eat a diet containing about 100 grams of fat per day and then collect all your stool over 72 hours. More than 7 grams of fat per day (or 21 grams total over the three-day collection) indicates fat malabsorption, which can point to pancreatic problems, celiac disease, or other conditions affecting the small intestine.
How to Collect and Store Your Sample
Proper collection matters because a contaminated or degraded sample can give unreliable results. Most labs provide a collection kit with a clean container and sometimes a preservative solution. The general rule is to avoid contaminating the sample with urine or toilet water. Many kits include a plastic “hat” that sits in the toilet bowl to catch the stool cleanly.
Timing depends on what’s being tested. Bacterial cultures and parasite samples are stable at room temperature and should reach the lab within 72 hours. C. difficile samples should be refrigerated if you can’t deliver them within an hour, but they remain stable for up to three days in the fridge. Samples being tested for white blood cells (fecal leukocytes) need to get to the lab immediately, as these cells break down quickly.
For occult blood tests, your doctor may ask you to avoid certain foods or supplements for a few days beforehand, particularly if you’re doing the older guaiac-based version, which can react to red meat, vitamin C, and iron supplements. FIT testing is less affected by diet, though medications like proton pump inhibitors are still worth mentioning to your doctor before the test.