The course of an infection with the microsporidian Encephalitozoon cuniculi in a colony of captive emperor tamarins (Saguinus imperator) is described. In two litters, the infection was associated with overt disease and death of all infants. Immunohistochemistry for E. cuniculi showed generalized infections, and histopathologic evaluation revealed systemic vasculitis and disseminated mixed inflammatory cell infiltration with and without necrosis in several organs. Serologically, some of the juvenile animals presented with high titres for Encephalitozoon, while the adults had low titres. The E. cuniculi "dog strain" was identified by molecular means for the first time in Europe. The origin of the infection appeared to be a pair of breeding adults that originated from the US. Our data suggest that the organism persisted over years in the colony, and that subclinically infected animals most likely were involved in perpetuating the infection. Efforts should be made to ascertain if this microorganism is present in other captive populations of this endangered monkey species and to prevent its further spreading.