Gender differences in body composition, the prevalence in overweight and obesity as well as in physical activity patterns were tested among 3003 children and adolescents aging between 6 and 18 years (x = 12.1 +/- 3.6) in Vienna and rural parts of Eastern Austria. As to be expected, the absolute and relative amount of body fat was significantly higher among girls of nearly all age groups, while boys exhibited a significantly higher amount of lean or fat free body mass. The prevalence of overweight and obesity was markedly higher among prepubertal girls, however significantly lower among younger and older adolescent girls aging 11 years and older in comparison to their male counterparts. This was however only true of adolescents originating from Austria. Considering adolescents with a background of migration originating from Turkey or the Near East, a significantly higher amount of overweight and/or obesity was found among girls. Therefore, biocultural factors have to be considered to explain gender differences in obesity during childhood and adolescence.