This study examined the change of body composition in Japanese university students. Subjects were university students divided into two groups by sex for two different time periods: 67 males and 46 females for 1986-1987 and 47 males and 64 females for 1994-1995. Body height, weight, and underwater weight were measured to estimate the percentage of body fat. The fat mass index (FMI) was applied after adjusting fat mass and the fat-free mass index (FFMI) applied after adjusting fat-free mass for body physique by dividing (body height)2. The mean body mass index (BMI) increased from 1986-1987 to 1994-1995 in males and decreased in females, although there were no statistical differences between two time periods in both sexes. The FMI indicates that in 1994-1995 males had significantly more fat adjusted for body height than in 1987. Females in 1994-1995 had significantly less FFMI than those in 1986 despite FMI similar to that of 1986. Our results thus warn against a trend toward excessive thinness in collegiate females and insufficiency of evaluating body composition using the BMI alone.