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To investigate the longitudinal associations of cardiorespiratory fitness (CRF), motor competence (MC), and body fat percentage (BF%) with cognition in children.Altogether 371 children (188 boys, 183 girls) aged 6–9 years at baseline participated in this 2-year follow-up study. We assessed CRF by maximal cycle ergometer test, computed the MC score from the z-scores of 50-metre shuttle run, static balance, and box and block test results, measured BF% by dual-energy X-ray absorptiometry, and assessed cognition using the Raven’s Coloured Progressive Matrices (RCPM) score. The associations were studied by linear regression analysis and analysis of covariance with repeated measures.In boys, a higher MC score (β=-0.161, 95% CI=-0.314 to -0.009), a shorter 50-metre shuttle run test duration (β=0.152, 95% CI=0.007 to 0.296), and a higher number of cubes moved in the BBT (β=-0.161, 95% CI=-0.309 to -0.013) at baseline were associated with a smaller increase in the RCPM score during follow-up. These associations were largely explained by the RCPM score at baseline. However, boys in the highest third (mean difference=2.5, 95% CI for difference=0.66 to 4.33) and the middle third (mean difference=2.1, 95% CI for difference=0.39 to 3.82) of the MC score at baseline had a higher RCPM score over the 2-year follow-up than boys in the lowest third. CRF, MC, or adiposity were not associated with the RCPM score in girls. Changes in CRF, MC, or BF% were not associated with changes in cognition.Higher MC at baseline predicted better cognition during the first two school years in boys but not in girls. CRF or adiposity was not associated with cognition in boys or girls.