Microsporidia are worldwide ubiquitous intracellular protozoan parasites infecting most major groups of the animal kingdom. In humans, microsporidiosis has recently emerged as a significant cause of morbidity in immunocompromised patients, and particularly in patients with acquired immunodeficiency syndrome (AIDS). Parasites of the genus Encephalitozoon cause keratoconjunctivitis and disseminated infections. In 15 to 30% of patients with advanced stage AIDS, Enterocytozoon bieneusi is the causative agent of major chronic diarrhoea. Clinical manifestations include numerous (2 to 8) and abundant, irregular liquid or semi-liquid stools without evidence of intestinal haemorrhage. Impaired absorption is aggravated by food intake causing the patients to restrain from eating and subsequent weight loss is progressive and irreversible. The diarrhoea becomes permanent and leads to dehydration ad malnutrition. Spontaneous remissions have been observed but are always of short duration. Microsporidiosis has also been found in ocular localizations in patients with AIDS; these keratopathies may be due to Encephalitozoon cuniculi, the only known species in mammals but E. hellem, a morphologically identical but antigenically different species has been identified. Other visceral localizations have been observed. Diagnosis of microsporidiosis relies on the demonstration of spores and/or intracellular parasites in stools, urine or tissue biopsies. The responsible agent can generally be identified by light microscopy, but differentiation between species still requires electron microscopy. New light and fluorescent microscopic techniques have been proposed for easier recognition of spores in various pathological samples. Immunodiagnostic techniques are limited due to the lack of correlation between antibodies detection and clinical manifestations. Although the parasite can be identified and although its cycle has been carefully studied, no prophylactic action can be taken because the mode of transmission remains largely unknown. Many treatment protocols have been tried but none have been found to be effective. Very little pharmacological data has been accumulated. Microsporidiosis is, and will remain, a major opportunistic infectious disease causing uncontrollable debilitating malnutrition in AIDS patients unless an effective treatment can be found, a major challenge for medical science.