Background: Prevalence of obesity increased noticeably during the last decades. Little is known so far about the association between fat accumulation due to obesity and skeletal muscle mass. The aim of this study was to describe the association between fat mass and muscle mass after adjusting for relevant confounding factors in the National Health and Nutrition Examination Survey (NHANES) study population of children and adolescents. We postulated a negative correlation between fat mass and lean body mass. Methodology: A total of 849 whole body DXA-scans of the NHANES study population of children and adolescents aged eight to twenty years of the years 1999-2004 were eligible for statistical analysis. Appendicular lean body mass (appLBM) was used to evaluate muscle mass. Bivariate analysis (Pearson's correlation coefficient), multiple linear regression analysis and mediation analysis were performed. The multiple regression analysis and mediation analysis were adjusted for weight, age height, sex ethnicity and physical activity. Results: Fat mass correlates with appendicular lean body mass (Pearons's r 0.336, p < 0.001). In the multiple linear regression analysis the regression coefficient between appLBM and FM was positive (0.204; p < 0.001), when considering appendicular lean body mass, fat mass and body weight, the regression coefficient was negative (-0.517; p < 0.001). Conclusions: Study results indicate a negative association of fat mass and skeletal muscle mass in children and adolescents, when weight, age, height, sex ethnicity and physical activity are considered. Further investigations are needed to evaluate if there is a biochemical interaction between fat cells and muscle cells that could explain this effect.