The importance of cognitive health for academic success is well-recognized. However, longitudinal data regarding the associations of body fatness, physical fitness and cognition are relatively scarce and mixed. The purpose of this study was to investigate whether body fatness, cardiorespiratory fitness (CRF) and muscular fitness (MF) in preschool are associated with cognitive skills in first grade at school. 133 South Estonian children aged 6-7 years were recruited from 13 kindergartens and again at 7-8 years when they had entered school. Body fat percentage (BF%), CRF, MF as the mean of z-scores of relative handgrip strength and standing long jump tests, and cognitive skills (verbal, conceptual, perceptual) were studied. There were no associations between BF% and CRF in pre-school with perceptual, conceptual or verbal skills in school in boys and girls. In boys, higher MF in preschool predicted higher verbal skills (β = 0.293, p = 0.021) in school after adjustment for con-founders. Cognitive skills at baseline seemed predominantly predict later cognitive performance in school. In conclusion, higher muscular fitness in preschool predicted better verbal skills in first grade at school in boys but not in girls. Body fatness and cardiorespiratory fitness in preschool were not associated with cognitive skills in school.