PURPOSE: To verify the association of motor skills with habitual and organized PA participation, and sedentary behavior for males and females. METHODS: The study employed a cross-sectional design in a sample of seventy-six second graders from a public elementary school in a Midwestern State. RESULTS: Mann Whitney and t-tests indicated gender differences in FMS and PA variables. Spearman correlation analyses demonstrated that habitual PA was correlated to total FMS, and manipulative skills for boys. For girls, a significant association was present in organized PA and locomotor skills. CONCLUSION: Choice of organized physical activity seems to influence the development of FMS and affect habitual PA behavior differently in boys and girls.