An enzyme-linked immunosorbent assay (ELISA) was used to detect antibodies to Encephalitozoon cuniculi in man, using spores derived from tissue culture as antigen. Negligible cross-reactions were found with other microsporidia of vertebrate or of invertebrate origin and there was no cross-reaction with Toxoplasma gondii, using ELISA, immunoperoxidase or immunofluorescence staining. A high prevalence of antibodies to E. cuniculi was found in patients suffering from schistosomiasis, malaria and neurological and psychiatric disorders, but not in healthy individuals.