The current status of Helicobacter contamination of laboratory mice, rats, gerbils, and house musk shrews from 47, 10, 4, and 3 colonies, respectively, in Japan was studied. Helicobacter was detected by reverse transcription (RT)-nested polymerase chain reaction (PCR) with Helicobacter genus-specific primers by using feces obtained from the animals. H. hepaticus, H. muridarum, H. bilis, H. rodentium, "Flexispira rappini", and "H. suncus" were identified with species-specific primers. Other species of Helicobacter were identified by sequencing of PCR products amplified with genus-specific primers. For mice, H. hepaticus, H. bills, H. rodentium including H, rodentium-like organism,"H. typhlonicus"-like organism, and H. westmeadii-like organism were detected from 12 (25.5%), 1 (2.1%), 18 (38.3%), 1 (2.1%), and 1 (2.1%) colonies, respectively. Forty-seven (5.7%) mice from six (12.8%) colonies were contaminated with both H. hepaticus and H. rodentium. H. rodentium was detected in rats from three (30.0%) colonies. In gerbils, H. hepaticus was detected in three (75.0%) colonies, but other species of Helicobacter were not detected. In house musk shrews, "H. suncus" was detected in animals from two (66.7%) colonies. Visible lesions in the liver, which showed multiple pale to white foci, were observed in 6/42, 5/174, and 1/21 mice infected with H. hepaticus, H. rodentium, and H. hepaticus/H. rodentium, respectively, and 1/14 gerbils infected with H. hepaticus. The results suggest the prevalence of these species of Helicobacter in mice, rats, gerbils, and house musk shrews in Japan.