Human stool contains a myriad of microorganisms, of which the vast majority are nonpathogenic and represent an important component of the healthy microbiome. The increasing use of molecular techniques has allowed the rapid identification of bacteria, viruses and parasites in human stool. This review focuses on the 3 main classes of parasite responsible for human disease, helminths, protozoa and ectoparasites, and highlights the importance of differentiating between pathogenic and nonpathogenic parasites.