Sexual dimorphic characteristics, which play an important role in human evolution studies and biological research, can be studied morphologically and metrically. Geometric morphometrics allows a better assessment of morphological characteristics. Statistical shape analysis has a long history in neuroanatomical and other research. The aim of this study was to identify shape differences of the corpus callosum between genders. Landmark coordinate data were collected from two-dimensional magnetic resonance imaging scans of 93 homogeneously aged patients, 45 men and 48 women. These data were analyzed using Euclidean distance matrix analysis and thin plate spline analysis. The general shape variability of the corpus callosum of men was greater than that of women (men, 0.134; women, 0.097). We found no significant difference between sexes in the general shape of the corpus callosum, but we did find significant differences in the distances between some landmarks. Deformation of the corpus callosum between men to women was mainly detected in the posterior of the corpus callosum. These results serve as a reference for future studies on shape alterations of the corpus callosum associated with certain conditions.