Regional differences in IQ are estimated for 47 prefectures of Japan. IQ scores obtained from official achievement tests show a gradient from north to south. Latitudes correlate with height, IQ, and skin color at r = 0.70, 0.44, 0.47, respectively. IQ also correlates with height (0.52), skin color (0.42), income (0.51) after correction, less homicide rate (− 0.60), and less divorce (− 0.69) but not with fertility infant mortali'ty. The lower IQ in southern Japanese islands could be attributable to warmer climates with less cognitive demand for more than fifteen hundred years.