Craniometric analyses were employed to assess the degree of variation among previously recognized Ainu populations. Heterogeneity among populations was evaluated by calculating the contribution of among-group variation to total variation. The analyses were designed to investigate the hierarchical population structure represented by River groups within Province groups. River groups were defined in previous ethnological studies and were regarded as strongly isolated social units. However, univariate and multivariate analyses did not support this view. Cranial heterogeneity was most apparent in comparisons of Province groups composed of several River groups. The degree of heterogeneity was statistically greater than that among all River groups and was also greater than that among archaeological Jomon populations from Honshu. The great heterogeneity among Province groups was also supported by pair-wise distance analysis. The pattern of variation revealed by principal component analysis was different for each sex. The main contribution to regional variation was provided by male facial measurements. These results give a baseline for discussion about Ainu population history and microevolution, adaptation to different environments, intermarriage, and admixture with foreign populations.