Background: Childhood motor skills are important not only for the physical and mental health of children, but also for the prevention of future lifestyle diseases. This study aimed to investigate how motor skills among first-grade children in Japan are associated with dietary and lifestyle habits, after adjustment for various confounding factors.Methods: First-grade children (aged 6-7 years) attending three public elementary schools in Tokyo, Japan (n=884), participated in this cross-sectional study. Homeroom teachers distributed self-administered questionnaires to parents and children. Questionnaires focused on lifestyle habits and required completion of a 1-day dietary record. Motor skills were measured by the New Physical Fitness Test (NPFT). Physique was calculated using Rohrer’s index formula: weight (kg) / height (cm) 3 × 107. Multiple regression analysis was used to investigate the association between NPFT score and determinant factors. We also examined the association between NPFT score and the amount of energy derived from a healthy diet versus snacks.Results: NPFT scores were significantly and positively correlated with involvement in exercise lessons (boys, β = 0.131, P = 0.006; girls, β = 0.121P = 0.012), total energy intake (boys, β = 0.096, P = 0.041; girls, β = 0.145, P = 0.003), and outside playtime in boys (β = 0.135), and negatively correlated with Rohrer’s index in girls (β = -0.097, P = 0.047). Moreover, the amount of energy derived from a healthy diet showed positive correlations with NPFT score (boys, β = 0.120, P = 0.011; girls, β = 0.137, P = 0.005).Conclusions: Children’s motor skills were associated with the Rohrer’s index, involvement in sports lessons, outside playtime, and total energy intake, particularly that derived from a healthy diet. These results suggest that a well-balanced diet including grains, vegetables, fish and meat, fruits, and milk, is important for improving children’s motor skills.