There is a north-south gradient in the body heights of Japanese children. A hypothesis had previously been proposed that differences in thyroid hormone activity induced by geographical differences in effective day length (duration of photoperiod exceeding a predetermined light intensity) might cause the differences in height. If thyroid hormone is involved, the effect should extend to body weight. This study examined whether geographical differences in body height and weight can be explained in terms of thyroid hormone activity induced by geographical differences in the photoperiodic environment using prefecture-level anatomical data and Japanese Mesh Climatic Data. Multiple regression analysis demonstrated that the combination of effective day length and weight was statistically significant as a predictor of height. Controlling for body weight revealed that effective day length was inversely correlated with height. Multiple regression analysis revealed that a combination of effective day length and height was statistically significant as a predictor of weight. Controlling for height demonstrated that effective day length was positively correlated with weight. Assuming an inverse correlation between effective day length and thyroid hormone activity, these results appear to show that short day-length will increase the activity of thyroid hormone and contribute to increasing height, but will inhibit weight gain; in contrast, long day-length will decrease the activity of thyroid hormone and contribute to increasing weight but will inhibit height gain. Geographical differences in height, and weight, and part of the prevalence of obesity in Japanese children and early adolescents may be explained by geographical differences in effective day length.