The microsporidian Encephalitozoon cuniculi can infect a wide variety of mammals including man. In this study, E. cuniculi isolates of animal origin were compared with 6 isolates obtained from HIV-infected patients. Based on results of Western blot analysis, random amplified polymorphic DNA (RAPD) and the sequence of the rDNA internal transcribed spacer (ITS) the isolates were classified into 3 groups with the repeated element 5'GTTT-3' in the ITS being a reliable genetic marker. Five isolates from Swiss patients were found to be homologous to isolates from Swiss rabbits (strain I). The sixth isolate from a patient from Mexico differed by all methods and could be attributed to E. cuniculi strain III that has been described from 2 dogs from the USA. All of these isolates were distinguished from isolates from blue foxes from Norway (strain II). Intraspecific nucleotide divergence of the SSU rRNA gene of E. cuniculi belonging to the 3 strains was in the same low range (0.00-0.15%) as was found for the corresponding sequence of 2 E. hellem isolates. Groups of 2 rabbits were infected by oral inoculation of 10(7) E. cuniculi spores (2 isolates from strain I of human and rabbit origin, 1 from strain III) as shown by antibody responses and the re-isolation of the parasites from brain material. The results provide further evidence that per oral transmission of the parasite between various hosts is feasible.