Various tools for identifying potentially inappropriate medications (PIMs) have been developed. This 5-year prospective cohort study of 196 elderly patients receiving home-based medical services in Japan compared the use of two tools for identifying PIMs, the American Geriatrics Society’s Beers Criteria and the relatively new Screening Tool for Older Person’s Appropriate Prescriptions for Japanese (STOPP-J), to determine the impact of PIMs on hospitalization and mortality rates. PIMs categorized by STOPP-J were associated with hospitalization and mortality, whereas Beers Criteria PIMs were associated with hospitalization only after excluding proton pump inhibitors.