One concern about rotavirus vaccines is its possible association with intussusception. Thus, it is necessary to determine the baseline incidence for intussusception in the first year of life in places where rotavirus vaccines are introduced. However, few safety data exist for the period at which the first dose of Rotarix and RotaTeq are allowed to administer in Japan. The first dose of Rotarix is scheduled to administer at 6–20 weeks of age and that of RotaTeq is scheduled to administer at 6–24 weeks of age; the upper limits for these vaccines is later than the upper limit recommended by the World Health Organization by 5 and 9 weeks, respectively. We performed a retrospective cross-sectional study by reviewing medical charts of all hospitals that provided pediatric beds in Akita Prefecture, Japan, and identifying the cases of intussusception that met the Brighton criteria level 1 in these hospitals between January 2001 and December 2010. During this 10-year period, 122 children younger than 1 year of age were diagnosed with intussusception. The incidence of intussusception was estimated at 158 per 100,000 person-years among children younger than 1 year (95% confidence interval, 131–188), 10 per 100,000 person-years for children aged 0–2 months, 165 for children aged 3–5 months, and 300 for children aged 6–8 months. This rapid and substantial increase in the incidence of intussusception during the first year of life should be considered when formulating the immunization schedule for administering rotavirus vaccines in Japan.