In order to better understand the possible impact of second-generation rotavirus vaccines on the incidence of intussusception (IS), robust knowledge of the baseline childhood epidemiology of IS from various sources is essential. This study estimated the overall and agespecific baseline incidence of IS among young Japanese children. Data on 57 IS cases from 42,438 screened children aged less than 12 months, born between January 2005 and April 2011 and covered by the health insurance claims database were retrospectively extracted (NCT01479491). IS cases were identified using the International Classification of Diseases, 10^th revision (K56.1), with relevant examination and procedural codes. The extracted data were used to estimate the incidence of IS. Among all IS cases extracted, 51 (94.4%) were confirmed IS, of which 49/51 (96.1%) were hospitalized, 2/51 (3.9%) visited outpatient wards; 26/51 (51.0%) were males. The overall incidence of confirmed IS and IS hospitalizations among children aged less than 12 months was 143.5 (95% CI: 106.8 - 188.6) and 137.8 (95% CI: 102.0 - 182.2) per 100,000 children-years, respectively. Three (5.9%) IS cases were identified in children aged below 3 months. IS cases peaked between 6 - 11 months of age (40/51 [78.4%]) with the highest incidence (321.5 [95% CI: 138.8 - 633.4] per 100,000 children-years) observed at 10 months of age. The overall recurrence rate of IS was 3.7% (95% CI: 0.5 - 12.7). The baseline incidence of IS in Japanese children aged less than 12 months was higher than that observed in other countries prior to the introduction of second-generation rotavirus vaccines.