Genital structures are among the most variable in nature and have been suggested to evolve at exceptionally high rates. However, the vast majority of research on genital morphology has been done on male genitalia. We present one of the few studies of female genital shape using geometric morphometrics, and the first of such studies to employ 3D geometric morphometrics, using the spiny dogfish shark, a taxon for which reproductive biology is well‐studied. In a sample of 21 adult females, we found no correlation between body size and reproductive and non‐reproductive trait size, and therefore no general allometric patterns. Furthermore, we found limited evidence for different 2D and 3D vaginal shapes in visibly pregnant and not visibly pregnant sharks, but trends were more obvious in 3D than 2D. We found high congruence between data derived using 2D geometric morphometrics with that derived from 3D methods. We also found exceptionally high asymmetry in the vagina, again more apparent in 3D than in 2D. Visibly pregnant sharks had especially high directional asymmetry (>48% of total variation) likely as a result of an asymmetric distribution of pups in the shark's paired oviducts. Therefore, this asymmetry was functional rather than developmental and presents an important consideration when studying vaginal shape. The lack of significant association between pregnancy and vaginal shape in a species with an extremely long pregnancy suggests that vaginal shape differences may be under additional selective forces such as sexual antagonism during copulation. A combination of 3D geometric morphometric methods along with assessments of asymmetry sheds further light on the growing appreciation that female genitalia is highly variable in shape and may play a substantial role in sexual selection.