Normally the stool is firm or semi-formed and is coloured varying shades of brown. It may be possible to recognize undigested food particles and their frequency reflects the nature of the diet, the amount of mastication and the degree of intestinal hurry. The shape of the stool varies greatly and is of little diagnostic significance.

Blood from anorectal diseases is seen as streaks on the surface of the stool. Blood from lesions higher up the colon will be intimately mixed with the stool, as is characteristically found in inflammatory bowel disease. The passage of pure blood with no faecal material may occur in polyps, haemorrhoids, colonic cancer, diverticular disease, infarction of the colon and intussusception. Patients with bleeding peptic ulcers occasionally pass bright red, unaltered blood per rectum. The stools may be coloured red after the ingestion of beetroot.

The stools are pale in the presence of intra- and extrahepatic cholestasis and in severe steatorrhoea. Tarry black melaena stools indicate the partial digestion of blood in the gastrointestinal tract. The appearance is usually characteristic, but if there is any doubt the stool is mixed with a small volume of water which will be coloured red. Chemical tests for blood should be performed. Iron-containing stools are grey-black, and this can usually be distinguished from melaena. Other causes of black stools include the ingestion of charcoal, bismuth compounds and large quantities of liquorice.

In cholera the stools are virtually colourless and liquid, and contain flakes of mucus, shed epithelial cells and enormous numbers of vibrios (‘rice water’ stool). A very similar appearance is seen in staphylococcal enterocolitis, which may be readily diagnosed by a Gram stain of the faecal material, when numerous clumps of bacteria are seen.

Various intestinal parasites may be seen by the naked eye in the stool including tapeworms (Taenia solium or saginata), roundworms (Ascaris lumbricoides), and threadworms (Enterobius vermicularis).

A microscopic examination of a stool suspension is required to diagnose pathogenic protozoa and helminthic ova. Stool can be obtained from a bedpan or other container; it is also possible to use material removed from the glove after performing a rectal examination. A wooden applicator is used to place a pea-sized portion of stool on a microscope dish previously moistened with two or three drops of isotonic saline. A coverslip is applied carefully to ensure that no air bubbles are trapped. The slide is scanned under low power, particularly at the edges. Entamoeba histolytica and Entamoeba coli can exist in vegetative and multinucleate cystic forms; the biflagellate Giardia intestinalis may be identified, although it is more readily found in the duodenal aspirate; and Enterobius vermicularis can be demonstrated. Ova which may be seen include Ascaris lumbricoides, Ankylostoma duodenale, Necator americanus, Taenia saginata, Taenia solium, Enterobius vermicularis, and Strongyloides stercoralis. It may be necessary to undertake repeated examinations of the stool. Stools should always be collected and examined before a barium examination. Commercial stool collection kits are available which contain preservatives for parasites and cysts.

A number of crystals are normally seen in the stool, but they are not of diagnostic significance.