We used restriction endonuclease analysis of plasmids (REAP) and pulsed-field gel electrophoresis (PFGE) to investigate clusterings of methicillin-resistant Staphylococcus aureus (MRSA) infections in our orthopedic unit, neurosurgery unit, intensive care unit, and burn unit. Fourteen different strain types were identified by REAP and 10 different strain types were identified by PFGE among 25 MRSA isolates collected during these incidents of infection. Though neither technique was clearly superior to the other for typing MRSA isolates, REAP is recommended as a relatively simple and reproducible technique for the preliminary investigation of MRSA infection outbreaks in clinical settings.