This article outlines the principal gastrointestinal protozoal diseases that have been recorded as affecting reptiles. It covers 9 genera of flagellates/amoebae, 1 ciliate genus, and 5 genera of coccidia, describing their pertinent anatomy and what is known about their epidemiology, including clinical presenting signs and intestinal pathological changes. The agents are initially discussed individually and, to avoid repetition, common information about diagnostics, treatment, and control is then presented.