We previously revealed the prevalence of strabismus and amblyopia in elementary school children between 6 and 12 years of age in Japan in the year 2003. Questionnaires asking the number of children with different types of strabismus and amblyopia were sent to all elementary schools in Okayama Prefecture in the year 2005, and the results in the year 2005 were compared with those obtained in the year 2003. The number of children covered by the return of questionnaires was 84,619 (74%) of 113,763 total pupils, including grades I to 6, in Okayama Prefecture in the year 2005. The total numbers of children with strabismus and amblyopia, including grades I to 6, were 844 (0.99%, 95% confidence interval: 0.94-1.06%) and 173 (0.20%, 95% confidence interval: 0.17-0.23%), respectively. The numbers of children with any type of exotropia and any type of esotropia were 524 (0.62%) and 187 (0.22%), respectively. In the previous survey conducted in 2003, the number of children covered by the return of questionnaires was 86,531 (76%) of 113,254 total pupils. The total numbers of children with strabismus and amblyopia, were 1,112 (1.28%, 95% confidence interval: 1.24-1.36%) and 125 (0.14%, 95% confidence interval: 0.12-0.17%), respectively. The numbers of children with any types of exotropia and esotropia were 602 (0.69%) and 245 (0.28%), respectively. The prevalence of strabismus in this large population of Japanese elementary school children was significantly different between the years 2003 and 2005, while the prevalence of amblyopia was similar between the years.