Intestinal protozoan infections are still highly prevalent world-wide both in industrialised and unindustrialised countries, but especially in the latter where they may be the cause of important morbidity and mortality. Although most of them have been an ever-present threat to mankind; others have emerged and re-emerged in a manner that was previously unsuspected. The scope of these intestinal protozoan infections presenting to the doctor office is quite diverse. Most of them may cause acute or chronic diarrhoea in healthy individuals and may result in intractable, life-threatening illness in patients with immunosuppressive diseases, like acquired immunodeficiency syndrome. Due to the lack of vaccines to avoid these infections, adequate identification and treatment of these infections may result in significant benefit for individual patients and public health. This article presents an update on the current most important points of pharmacotherapy available at present against amoebiasis, balantidiasis, giardiasis, dientamoebiasis, Blastocystis hominis infection, cryptoporidiosis, cyclosporiasis, isosporiasis, sarcocystosis, and microporidiosis.