Skeletal muscle is an important body compartment in obesity, because low energy expenditure results from decrease in the proportion of metabolically active tissues such as skeletal muscle. Lean body mass（LBM）and body fat mass（BFM）may change in childhood obesity, but less is known about the characteristics of body composition, skeletal muscle and body fat mass in the body trunk and extremities in obese children without habitual physical activity（HPA). We investigated the differences in LBM, BFM and the cross-sectional areas（CSAs）of skeletal muscle, visceral and subcutaneous fat in body regional and trunk between male obese children with and without HPA. LBM and BFM was determined by air-displacement plethysmography in Japanese male obese children without (n=21, 9.6+/-1.4 years old) and with (n=23, 9.7+/-1.3 years old) HPA. The CSAs of skeletal muscle, visceral and subcutaneous fat located in upper arm, thigh and trunk, respectively, were determined using magnetic resonance imaging. Obese children without HPA showed significantly higher BFM/height2 and lower LBM/height2 than obese children with HPA (p<0.05). In obese children without HPA, the CSAs were significantly higher in visceral fat and lower in skeletal muscle of thigh than obese children with HPA when adjusted by BFM0.67 or LBM0.67 (p<0.05).The present results indicate; (1) There may be difference of body composition, skeletal muscle and body fat mass in the body trunk and extremities in male obese children with/without HPA.; (2) Male obese children without HPA may have greater BFM and abdominal visceral fat, lower LBM and thigh muscle mass compared with obese children with HPA.