Microsporidia are ubiquitous organisms that are emerging pathogens in humans. These are most likely zoonotic and/or waterborne infections. In the immunosuppressed host, such as those treated with immunosuppressive drugs or infected with human immunodeficiency virus particularly at advanced stages of the disease, microsporidia can produce a wide range of clinical diseases. The most common manifestation is gastrointestinal tract infection; however, encephalitis, ocular infection, sinusitis, myositis and disseminated infection have also been described. In addition, these organisms have been reported in immune competent individuals. Multiple genera are involved in these infections and different organisms can result in distinct clinical pictures. Differences in clinical and parasitologic response to various therapeutic agents have emerged from clinical, as well as in vitro and in vivo studies. Currently there are no precisely defined guidelines for the optimal treatment of microsporidial infections. This article reviews the available data on compounds with in vitro activity and/or in vivo efficacy for microsporidial infections. Copyright 2000 Harcourt Publishers Ltd.