Enterocytozoon bieneusi is the most frequently found microsporidium in human infections. In all, 3 distinct genotypes were detected in 12 stool samples from 8 patients with acquired immunodeficiency syndrome (AIDS). A total of 9 polymorphic sites were found in the 243-bp-long internal transcribed spacer (ITS) of the rDNA gene, whereas none was found in 241 bp of adjacent rRNA coding regions. The genotype was stable in samples taken during 11 weeks of infection from one of the patients. The existence of and the ability to discriminate among strains of E. bieneusi are important prerequisites for elucidation of the hitherto unknown reservoirs of this pathogen and the mode of its transmission and may explain its pathogenicity.