The goal of this study was to investigate differences in physical fitness and sports participation over two years in children with relatively high, average, and low motor competence. Physical fitness and gross motor coordination of 501 children between 6-10 years were measured at baseline and baseline+2 years. The sample compromised 2 age cohorts: 6.00-7.99 and 8.00-9.99 years. An age and sex-specific motor quotient at baseline testing was used to subdivide these children into low (MQ < P33), average (P33 ≤ MQ < P66) and high (MQ ≥ P66) motor competence groups. Measures of sports participation were obtained through a physical activity questionnaire in 278 of the same children. Repeated Measures MANCOVA and two separate ANOVAs were used to analyze differences in changes in physical fitness and measures of sports participation respectively. Children with high motor competence scored better on physical fitness tests and participated in sports more often. Since physical fitness levels between groups changed similarly over time, low motor competent children might be at risk for being less physically fit throughout their life. Furthermore, since low motor competent children participate less in sports, they have fewer opportunities of developing motor abilities and physical fitness and this may further prevent them from catching up with their peers with an average or high motor competence.