Childhood overweight/obesity is growing steeply, globally. It is usually regarded as a risk factor for severe obesity over life-time course. Here, we investigated temporal course of overweight/obesity development in Japanese school children. A six-year longitudinal study was performed on 16,245 Japanese primary school children (8,427 boys and 7,818 girls) comprising three cohorts of 1(st) approximately 3(rd) grade. A baseline survey was conducted at 2001, followed by annual baseline studies from 2002 approximately 2007 to determine the prevalence and track overweight/obesity. Our results showed that the prevalence of overweight was 15 approximately 23% in boys and 15 approximately 18% in girls, however, for obesity it ranged between 4 approximately 7% in boys; and 2 approximately 4% in girls. As regards for tracking status, 60 approximately 80% of overweight and 35 approximately 70% of obese Japanese primary school boys track into overweight or obese junior high school adolescents. However, these percentages are lower among primary school girls, where only 50 approximately 70% overweight and 30 approximately 60% obese primary school girls track into overweight and obese adolescents, respectively. We conclude that Japanese boys are fatter than girls; and approximately 80% of overweight/obese Japanese primary school children track into junior high school overweight/obese adolescents.