Pathogenic intestinal protozoa are responsible for clinically important infections in both the developed and developing world. Treatments have been available for several decades for giardiasis, isosporiasis and amoebiasis, but until recently there were no effective remedies for the intestinal coccidia—cyptosporidium, microsporidium and cyclospora. In this Review, the author discusses the various pathogenic intestinal protozoa and the treatment options available.