In this study, we investigated whether the variant of the beta3-adrenoceptor gene is associated with accumulation of body fat in Japanese junior high school students. A total of 87 junior high school students, 50 boys and 37 girls, participated in this survey. The beta3-adrenoceptor gene variant was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Accumulation of body fat was assessed by skinfold thickness at the triceps and subscapular with a skinfold caliper. There was no difference between boys and girls in the frequency of the beta3-adrenoceptor gene allele. There were no significant differences in body mass index and percent body fat between the Arg carriers (Trp/Arg or Arg/Arg) and the Arg noncarriers (Trp/Trp) for either sex. The Trp64Arg variant of the beta3-adrenoceptor gene does not seem to have a strong effect on the accumulation of body fat in this group of Japanese junior high school students.