In Japan, the rate of low birth weight infants has increased, due to an increase in the number of women who smoke or are lean. A recent study showed that low birth weight was associated with a high adult waist-to-height ratio in adult Japanese women, but little data is available concerning children. In this cross-sectional study with 568 subjects (276 boys and 292 girls), we examined the association between birth weight and waist-to-height ratio in 7- or 8-year-old Japanese children, all born at full term. The mothers of the subjects responded to a questionnaire about the weight of the children at birth, and physical data were collected from the results of measurements conducted at each school. We divided the subjects into two groups by the median of the birth weight (3,000 g) by sex to elucidate the effects of birth weight on the waist-to-height ratio. There were 119 boys and 164 girls and 157 boys and 128 girls in the < 3,000 g and ≥ 3,000 g birth weight groups, respectively. The Mann-Whitney U test was used to compare the physical conditions in the two birth weight categories. Height was significantly lower in the birth weight < 3,000 g group among both the boys (P < 0.001) and girls (P < 0.001). The waist-to-height ratio was significantly higher in the < 3,000 g group in girls (P = 0.004), but not in the boys. Our results suggest that intrauterine environmental insults might have an effect on children, depending on sex.