Research indicates that children and adolescents gradually participate less in physical activity with age. Several factors are associated with children’s physical activity levels, such as motor performance, self-perception of athletic competence and motivation to physical activity. To gain a better understanding of the factors of importance for behavior related to an active lifestyle, the purpose of this study was to investigate the association between motor competence, physical self-perception and autonomous motivation and to examine to what extent this association may vary by sex. The sample consisted of 101 children, whose average age was 11.7 years (SD = 0.57), 53 boys and 48 girls. All subjects were measured on motor competence, physical self-perception and autonomous motivation for physical activity. The results indicate a low positive relationship between motor competence and physical self-perception for the entire sample and among girls. There is also a significant correlation between autonomous motivation and physical self-perception. No significant correlations were found between autonomous motivation and motor competence. The association between physical self-perception and autonomous motivation suggests that psychological factors play an important role in children’s participation in physical activity.