Physical inactivity is associated with poor physical fitness and increased body weight. This study examined the relationship between participation in organized sports and overweight as well as physical fitness in primary school children in southern Germany. Height, weight, and various components of physical fitness were measured in 995 children (7.6 ± 0.4 years). Sports participation and confounding variables such as migration background, parental education, parental body weight, and parental sports participation were assessed via parent questionnaire. Multiple logistic regression as well as multivariate analysis of covariance (MANCOVA) was used to determine associations between physical fitness, participation in organized sports, and body weight. Participation in organized sports less than once a week was prevalent in 29.2%, once or twice in 60.2%, and more often in 10.6% of the children. Overweight was found in 12.4% of the children. Children participating in organized sports more than once per week displayed higher physical fitness and were less likely to be overweight (OR = 0.52, P < 0.01). Even though causality cannot be established, the facilitation of participation in organized sports may be a crucial aspect in public health efforts addressing the growing problems associated with overweight and obesity.