To evaluate the relationship between human body composition and serum lipids levels, the distributions of subcutaneous adipose tissue (AT) and muscle thickness were evaluated in Japanese 449 males and 542 females, aged from 35 to 77 years. Among males, a significant positive correlation was observed between AT thicknesses and total cholesterol, and negative relationships between the AT and HDL-C as well as HDL-C/TC ratio. Among females, similar but weaker relationships were found for AT at the upper arm and trunk sites. However, the thigh AT thickness was positively correlated with HDL-C and HDL-C/TC ratio only among women. The muscle thickness in the abdomen and the thigh correlated significantly with HDL-C/TC for both sexes. Furthermore, the regional trend observed in both sexes remained significant after correction for concomitant variables such as age, tobacco and alcohol intake. We conclude that it is necessary to evaluate not only total body fat but muscle and AT thickness distributions when evaluating the relationship between body composition and serum lipids and lipoproteins.