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Obesity is considered to be epidemic worldwide. Stopping further progression interdisciplinary, outpatient intervention therapy programs for obese children have become increasingly important. FITOC (Freiburg Intervention Trial for Obese Children) consists of a combination of organized sports, behavioral therapy and nutritional advice. The effectiveness of the therapy is determined on the basis of anthropometrical and physical performance data. The purpose of this report is to give a differentiated view of the motor abilities of obese children and to describe changes in the course of the therapy program FITOC. Data were collected on n = 49 obese children (BMI > 97th percentile) aged 8 - 12 in a pretest at the beginning and posttest at the end of the intensive phase of the therapy. These data were compared with an age-matched German reference group. Besides the General Sports-Motor Test (Allgemeiner Sportmotorischer Test [AST]), the BMI-SDS values, the body fat mass (FM %) and the aerobic capacity (Watt/kg body weight) were recorded. In the pretest, the running exercise results and the aerobic capacity checked ranged significantly below the values of the reference group. The performance in the coordinative tests of the AST was differentiated. The medicine-ball toss was significantly above average of the reference group. In the posttest, the BMI-SDS values and the body fat mass (% FM) decreased (p < 0.001) and the aerobic capacity improved (p < 0.001). Performance in all motor abilities tests improved and the difference between the strength of the obese children and the strength of the reference group decreased. This study demonstrates that in obese children weight-bearing activities are below average but not all motor abilities.