By the time it has been through your intestines, most of the natural pigments in food have been digested away (the red from beetroot being a notable exception). The brown colour is due to a chain of processes, which begins with the breakdown of old red blood cells to produce a chemical called bilirubin. This ends up in the liver, where it mixes with bile. The bile travels into the gut, where bacteria metabolise the bilirubin into another chemical called stercobilin, which is brown.
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