Objectives: In this study Enterocytozoon bieneusi-positive faeces samples from AIDS patients in the north west of England were investigated by polymerase chain reaction (PCR) and DNA sequencing for potential zoonotic origins. Methods: The ITS and flanking regions of the rDNA was amplified by PCR and product sequenced. Sequences were compared with those held on GenBank to ascribe known genotypes. Results: Of 13 E. bieneusi-positive samples tested, all gave a 508 bp amplification product by PCR. The samples yielded the following: genotypes B (n = 11; so far only been found in humans), D (n = 1; has been reported from humans and a laboratory macaque) and K (n = 1; previously identified only from a cat). Conclusions: A possible zoonotic link with cats has been demonstrated for one human case. The origin of the majority of cases in the north west of England is unknown and may indicate that genotype B is solely a human pathogen.