BACKGROUND: Although diabetes mellitus is reported to be related to tooth loss, there is limited population-based evidence for this relationship. We investigated the actual situation of tooth loss by performing a population-based survey using information obtained from the National Database of Health Insurance Claims and Specific Health Checkups (NDB) in Japan. METHODS: Medical, dental and pharmacy claims data generated between 1 April 2015 and 31 March 2016 were obtained and analysed. Patients with medical and pharmacy claims of diabetes mellitus were allocated to the diabetes mellitus group. Patients with medical claims of acute upper respiratory inflammation, but without claims of diabetes mellitus, were allocated to the control group. The number of claims involving tooth loss, treatment of periodontal disease and visits to medical and dental institutions were obtained from the NDB. Descriptive statistics were used to compare the nature of tooth loss between patients with diabetes mellitus and the control groups. RESULTS: There were 5,248,405 patients in the control group and 1,570,082 patients in the diabetes mellitus group. Patients in the diabetes mellitus group showed a higher level of tooth loss than patients in the control group, among both sexes. Patients with diabetes mellitus tended to lose their posterior teeth at an earlier age than patients in the control group. Moreover, patients in the diabetes mellitus group showed greater tooth loss, regardless of whether or not periodontal disease was treated. CONCLUSION: Patients with diabetes mellitus show a higher level of tooth loss than those without diabetes mellitus, based on the results of a population-based survey.