Microsporidia are obligate intracellular, spore-forming protozoa and are regarded as newly emerging pathogens . Enterocytozoon spp. as well as Encephalitozoon spp. are recognized as major aetiological agents in chronic diarrhoea of immnunocompromised patients. The detection and differentiation of strains within microsporidial species is a prerequisite for the elucidation of their hitherto unknown reservoirs and their mode of transmission . In Enterocytozoon bieneusi, the most prevalent human-pathogenic microsporidium, 6 different genotypes of the internal transcribed spacer (ITS) of the rRNA gene are known so far, with 12 polymorphic sites . This pathogen has infrequently been detected in 2 animal hosts only, pigs and rhesus macaques, and only the genotype of the latter has also been found in a human patient, too. Encephalitozoon cuniculi has a wider confirmed spectrum of animal hosts, but only one polymorphic site is known in the ITS, differing in 3 different numbers of a tetranucleotide repeat. Therefore, further genomic targets may have to be characterized, too. Few data are available on strain differentiation in Encephalitozoon intestinalis and E. hellem.