In many teleost species, aragonite is the normal form of calcium carbonate in sagittal otoliths. In the case of one-side-only (OSO) vateritic otoliths (abnormal crystalline structure), morphological investigations are systematically conducted on the other side. The implicit assumption is that the morphological information on the aragonitic side remains unaffected by the presence of vaterite on the other side. However, the extent to which this assumption is met has never been explored. Applying geometric morphometrics on experimentally maintained brown trout (Salmo trutta) revealed incongruent variational patterns and mean shape differences between OSO and two-sided aragonitic otoliths, possibly due to trans-lateral compensation to preserve their auditory function. More specifically, fully aragonitic pairs of otoliths are more prone to exhibit microecological variations compared with OSO vateritic pairs. Simulation emphasizes the relative robustness of both micro- and macroecological effects until a high proportion of OSO vateritic otoliths is used. Given that otolith shape analysis provides a useful basis for stock separation, care should be taken when interpreting otolith shape in the presence of vateritic otoliths