The aim of this study was to investigate whether methicillin-resistant Staphylococcus aureus (MRSA) infections have spread among laboratory animals housed in our animal facility which is located close to the university hospital. Several epidemics of MRSA infection have occurred in the hospital, and we attempted to isolate these bacterial strains from the animals housed between 1994 and 2011. A total of 6,425 strains of S. aureus were isolated, of which 5,120 (79.7%) were isolated from rat feces. Only one MRSA isolate was subsequently detected in rats which were not treated with any antibiotics. The isolated MRSA harbored type II staphylococcal cassette chromosome mec (SCCmec), which was identical to that of a strain isolated at our university hospital. However, the coagulase type of the hospital isolates was II, which is the most endemic type in Japan, whereas our isolate was not identified to any coagulase type. These results indicate that MRSA is very rare in our animal facility, despite frequent contact between laboratory animals and medical school and hospital faculty.