Reverse transcriptase-polymerase chain reaction (RT-PCR) amplification of the nucleocapsid (N) gene of mouse hepatitis virus (MHV) successfully detected 36 strains from the faeces of mice that had been housed in animal facilities in Japan from 2000 to 2003. Subsequent restriction fragment length polymorphism (RFLP) analysis, using the enzymes Acc I, Alu I, EcoR I and Mbo I, demonstrated that these strains could be divided into five distinct subgroups and that the same MHV strains were detected from closely related mouse facilities. Furthermore, strains from the same facility showed the same RFLP pattern, irrespective of the year of detection, but this pattern varied between different locations. This study shows that RFLP analyses are a rapid and useful method for differentiation of MHV strains.