Background. The purpose of the present study was to investigate the relative contribution of upper and lower body obesity to obesity-related menstrual disorders. Methods. Women with polycystic ovary syndrome (PCOS) were excluded from the study. Eighty-three obese women with a body mass index (BMI, Wt/Ht(2)) of more than 25kg/m(2) were classified into two groups according to their menstrual status: one with menstrual disorders (n = 39; mean age+/-standard deviation, 31.6+/-4.9 years) and the other group (controls) with regular menstruation (n = 44; 32.2+/-4.4 years). Age, age at menarche, height, weight, and BMI were recorded. Trunk fat mass, leg fat mass, the ratio of trunk to leg fat mass amount (trunk-leg fat ratio), body fat mass, and the percentage of body fat were measured by whole-body scanning with dual-energy X-ray absorptiometry. Baseline characteristics and anthropometric variables were compared between the two groups. Results. Trunk-leg fat ratio in women with menstrual disorders was 1.48+/-0.29, which was significantly higher than that in controls (1.25+/-0.38, p<0.01). Trunk fat mass was also significantly higher in women with menstrual disorders than in controls (14.9+/-4.1 kg vs. 12.9+/-3.8 kg, p<0.05). However, BMI, percentage of body fat, body fat mass, and leg fat mass did not differ between the two groups. Age, age at menarche, height, and weight did not differ between the two groups. Conclusion. Upper body, but not lower body, obesity is associated with menstrual disorders.