A food poisoning (or "foodborne illness") infection is usually diagnosed by specific laboratory tests that identify a specific organism as the cause of illness. Bacteria such as Campylobacter, Salmonella, and E. coli O157 are found by culturing stool samples in the laboratory and identifying the bacteria that grow in the controlled environment of the lab. Parasites can be identified by examining stools under the microscope. Viruses are more difficult to identify, as they are too small to see under a light microscope and are difficult to culture. Viruses are usually identified by testing stool samples for genetic markers that indicate a specific virus is present.

Many foodborne infections are not identified by routine laboratory procedures and require specialized, experimental, and/or expensive tests that are not generally available. If the diagnosis is to be made, the patient must seek medical attention, the physician must decide to order diagnostic tests, and the laboratory must use the appropriate procedures. Because many ill persons to not seek attention, and of those that do, many are not tested, many cases of foodborne illness go undiagnosed. For example, the U.S. Department of Health and Human Services Centers for Disease Control and Prevention (CDC) estimates that 38 cases of salmonellosis actually occur for every case that is actually diagnosed and reported to public health authorities.