Introduction: The organ-system-based curriculum was developed in response to the demand for integrating basic sciences. It is an integrated curriculum with interdepartmental collaboration as an essential feature. We investigated its implementation in medical schools in Japan. Methods: The basic science/clinical medicine curricula of 80 medical schools were classified as either discipline-based or organ-system-based according to the self-report for the accreditation for medical education and the description in the latest version of “the Status Quo of the Medical School Curricula.” Results: According to the self-report, 12 schools introduced organ-system-based curricula in basic sciences and 52 in clinical medicine. Of the other medical schools, three in basic sciences and 16 in clinical medicine were classified as having an organ-system curriculum based on the “Status Quo of the Medical School Curricula.” Discussion: The concepts toward organ-system-based curricula differ between basic sciences and clinical medicine. The integration level of the organ system curricula is expected to increase in the future as subject committees and cross-departmental collaboration progress.