Leptin is a hormone that is synthesized and secreted by adipocytes. Leptin has been found to participate in a number of regulatory physiological functions. It suppresses food intake and increases energy consumption, increases blood pressure, and improves carbohydrate metabolism. The relationship between serum leptin concentration and percentage of body fat (% BF) in Japanese students in the 1st year of high school (1stHS, n = 889) and the 3rd year of high school (3rdHS, n = 948) was examined in a cross-sectional study. The mean of serum leptin concentrations showed no significant difference between the 1stHS and 3rdHS; it was significantly higher in girls than in boys in both grades. Significant gender differences were observed in both the slope and intercept of the regression lines. These results suggest that the serum leptin concentrations in Japanese high-school students do not differ significantly in the 1stHS and 3rdHS, but change with % BF, regardless of school year and the presence or absence of obesity.