The microsporidial species Enterocytozoon bieneusi is found among immunocompromised, particularly HIV-infected, patients with chronic diarrhoea, and rarely also among immunocompetent persons with self-limited diarrhoea. Only recently, E. bieneusi was detected in 4 pigs in Switzerland raising the question of a potential zoonotic nature of this parasite. We examined faecal samples of 109 pigs, 24 cows, horses and red foxes each for the presence of E. bieneusi by PCR and compared these isolates with isolates obtained from stool samples of 13 HIV-infected patients living in Switzerland. In animals, E. bieneusi was only identified in pigs with a prevalence of 35%. Analysis of the rDNA internal transcribed spacer (ITS) sequence allowed the classification of E. bieneusi from 28 pigs into 4 distinct genotypes which grouped very closely (identity 96.3-98.8%) together with 2 of the 3 human-derived E. bieneusi genotypes. Hence, E. bieneusi seems to be a common parasite in swine, but no genotypes were identified that were found in humans. Nevertheless, swine might serve as a new animal model for enterocytozoonosis.