A microsporidium of the genus Encephalitozoon was isolated into culture from the nasal epithelium of a patient with AIDS. It was compared with in vitro isolates of Encephalitozoon cuniculi and the type isolate of Encephalitozoon hellem by SDS-PAGE and by Western blotting with murine antisera raised to E. cuniculi, E. hellem and the nasal isolate, monoclonal antibodies raised to E. cuniculi and sequential sera from the patient. All tests showed similarities between E. hellem and the nasal isolate but differences between these two isolates and E. cuniculi. Minor protein differences between E. hellem and the nasal isolate were not considered sufficient to separate them at the specific level. The new isolate is named the Wainwright isolate of E. hellem. The ultrastructure of the Wainwright isolate in vitro was similar to that of the parasite in vivo but there was a greater tendency for disruption of the parasitophorous vacuoles. The deposition of the electron-dense surface coat on the sporogonic stages of E. hellem, as a uniform layer which later thickens, is in contrast to its deposition as broad bands, which later join up, in E. cuniculi. This may be a useful character in distinguishing the species without recourse to analysis of protein profiles.