There is limited information available on the association between Enterocytozoon bieneusi and diseases in animals or on the characteristics of the strains involved. This study examined the occurrence of E. bieneusi in piglets with and without diarrhea to determine its involvement. Among 472 fecal samples from 472 piglets (237 with diarrhea and 235 without) up to 7 weeks of age, 67 (approximately 14%) were polymerase chain reaction (PCR) positive for E. bieneusi. Of the 237 piglets with diarrhea, 38 (approximately 16%) tested positive for E. bieneusi. Of the 235 healthy piglets, 29 (approximately 12%) tested positive for E. bieneusi. This species was detected only in the younger group of piglets with diarrhea, particularly those aged less than 1 week and between 1 and 2 weeks. This suggests that E. bieneusi is a possible cause of diarrhea in piglets. This organism, however, produced asymptomatic infections in the older piglets, as there was no significant difference in the rates of occurrence between the diarrheic and nondiarrheic older piglets (aged older than 4 weeks). The internal transcribed spacer (ITS) region of the ribosomal ribonucleic acid gene of the ten E. bieneusi-positive samples was amplified using nested PCR and subsequently sequenced. Genetic polymorphisms, which were represented by five distinct genotypes (PEbA-PEbE), were found among the E. bieneusi isolates. The five genotypes identified in this study differed from each other by two to six single-nucleotide polymorphisms. Nine isolates from four genotypes (PEbA-PEbD) were homologous to previously known types that had originally been isolated from pigs. However, one isolate from the PEbE genotype was identical to type CAF1, which was originally isolated from humans. In addition, the phylogenetic relationships determined by the neighbor-joining analysis of the ITS sequences indicated this genotype to be more distant from the other pig-specific genotypes. Thus, this isolate from pigs may be distantly related to the pig-specific genotypes and may be capable of infecting humans.