A longitudinal study was conducted to assess associations between snack energy intake and either body mass index (BMI) or nutrient intake in Japanese children. A baseline survey was conducted with 243 children aged 6-7 y, and follow-up was performed 4 y later. Finally, 189 subjects were selected for the analysis. Snack intakes were obtained from self-administered records by guardians. The daily habitual whole dietary intake and exercise/sleep hours were obtained by questionnaires during the follow-up. Subjects were grouped into three, as per snack energy intake tertiles at baseline. Differences and linear trends between the three groups were tested for the mean values of snack energy intake, BMI, and nutrient density, 4 y after the baseline survey. In follow-up, the snack energy intake (kcal) in females was significantly higher in the intermediate (335±35, p<0.01) and high (318±32, p<0.05) groups than in low group (196±25). There was no significant difference in follow-up BMI in the three groups. However, after adjustment of the baseline BMI, a significantly positive linear trend (p<0.05) was observed in the follow-up BMI in females. There was no significant difference in total energy intake per day. In contrast, a significantly negative linear trend (p<0.05) was observed among the three groups in dietary nutrient density of calcium and vitamin A in females. These results suggest that, in females, a higher intake of snacks may affect the daily dietary balance, resulting in a higher BMI and lower mineral and vitamin intakes.