Overweight and obesity among children and adolescents are increasing. Fatty liver disease (FLD) is an emerging problem in this age group. We investigated prevalence of overweight and non-invasive FLD and associated clinical characteristics in a representative population-based sample of 378 children and adolescents aged 12-20 years who were randomly selected from the general population in Leutkirch, Southern Germany. Overweight was defined as having a body mass index above the 90th percentile for the respective age and sex. About 15% of female (29 out of 194) and 12% of male participants (22/182) were overweight. Among females, only one non-overweight individual showed signs of FLD but in more than one third of the overweight males (8/22) signs of FLD were present. Overweight subjects in general had an unfavourable lipid profile and abnormal concentrations of obesity-related hormones such as significantly lower concentrations of adiponectin and increased levels of inflammatory markers including C-reactive protein and fibrinogen. Overweight males with signs of FLD showed even more severe altered metabolic responses compared to those who were overweight without signs of liver injury. FLD was not explained by alcohol consumption or other chronic liver disease. In this sample of children and adolescents representative of the general population a high prevalence of non-alcoholic fatty liver disease (NAFLD) is found in overweight males. These individuals showed the most severe metabolic alterations compared to non-overweight and overweight individuals without NAFLD indicating even higher risk for future overweight and obesity-related diseases such as type 2 diabetes and cardiovascular disease.