Multivariate analysis of mandible measurements was applied to identify and to investigate the genetic relationships between 5 outbred stocks of female mice, Dlv: CD-1, Hg: CD-1, Crj: CD-1, CF-1 and Slc:ddY. (1) Principal component analysis revealed that CF-1 had a relatively large mandible with an obtuse muscular process and low anterior mandibular body, whereas Hg: CD-1 had a smaller mandible and exhibited intermediate values in terms of muscular process shape and anterior height. Crj: CD-1 showed a moderately large mandible and a higher anterior mandibular body. While the mandibles of Dlv: CD-1 and Slc: ddY were comparatively similar to each other in that they were both medium-sized, the former had an acute muscular process projecting posteriorly whereas the latter had a less prominent process. These morphological relationships between the 5 stocks determined by principal component analysis were generally in agreement with Mahalanobis’ distance between stocks based on the same mandible measurements. (2) According to the results of discriminant analysis, the frequency of misclassification was 11.4%, or 9/79 head when actual mandible measurements were used in categorization and 10.1%, or 8/79, when relative values, which exclude the size effect, were used. These data indicate that the genetic constitution of the 3 CD-1 stocks examined in this study differed from one another. (3) Based on dendrograms calculated from actual mandible measurements and relative values, Dlv: CD-1 was more closely related to CF-1 or Slc: ddY, which are derived from mice of other origins, than the CD-1 stocks examined in this study. Thus genetic monitoring seems to be essential for outbred stocks as well as for inbred strains.