Encephalitozoon cuniculi is a widespread and often sub-clinical microsporidian parasite of homeothermic animals, including man. The biology, pathology and taxonomy of the organism is reviewed and the available diagnostic methods discussed. Transmission is almost invariably via the oral route either by ingestion of contaminated tissues and other foods or by ingestion of infected urine, perhaps on food, or when animals lick the coats of others. Transplacental transmission does not seem common but can probably occur when susceptible animals are infected during pregnancy. It has been demonstrated once in mice and once in rabbits. The possibility of arthropod vector transmission awaits thorough investigation but this is unlikely to be as important as the oral route. No drugs have yet been found to be effective against E. cuniculi but control of the spread of encephalitozoonosis in laboratory animals, at least, can probably be achieved by maintaining laboratory hygiene.