PURPOSE: The purpose of this study was to assess relationship between IMF and physiological and biochemical variables. METHODS: Thirty-seven obese boys and girls participated in this study (age, 10.4 ± 2.1 years; height, 146.2 ± 13.4 cm; weight, 56.1 ± 16.5 kg; percentage of overweight, 41.1 ± 16.8%). This study was conducted a part of treatment of the subjects and was approved by the institutional review board of local committees. Computed tomography (CT) images were taken at the mid-thigh and umbilicus levels. Using the CT images, IMF index of the quadriceps femoris (QF), hamstrings (HM) and adductor (AD) muscle groups based on mean grey scale level of the interested muscle groups and visceral fat cross-sectional area (CSA) were calculated. For the mid-thigh CT image, skeletal muscle CSA and subcutaneous fat was also calculated. Plasma triglyceride, FFA, HDL-cholesterol, total-cholesterol, AST, ALT, glucose and HbA1c were measured from fasting blood drop. RESULTS: IMF index of QF, HM and AD was significantly different in all comparisons: HM was the lowest (1066 ± 6), meaning largest IMF depot, and QF was the highest (1080 ± 3), meaning smallest IMF depot. Stepwise regression analysis revealed that QF CSA, visceral fat CSA, and triglyceride were extracted to predict IMF index in QF (R=0.707, P < 0.01). For IMF index in HM, visceral fat CSA, age, triglyceride, percentage of overweight, and sex were extracted (R=0.806, P < 0.01). Interestingly, percentage of overweight was the only extracted variable to predict IMF index in AD (R=0.529, P < 0.01). CONCLUSIONS: These results suggest that muscle-specific IMF deposition pattern was observed in obese children and that intramuscular fat in each muscle group may have physiological and biochemical specific roles.