The bony labyrinth in the temporal bone houses the sensory systems of balance and hearing. While the overall structure of the semicircular canals and cochlea is similar across therian mammals, their detailed morphology varies even among closely related groups. As such, the shape of the labyrinth carries valuable functional and phylogenetic information. Here we introduce a new, semilandmark-based three-dimensional geometric morphometric approach to shape analysis of the labyrinth, as a major improvement upon previous metric studies based on linear measurements and angles. We first provide a detailed, step-by-step description of the measurement protocol. Subsequently, we test our approach using a geographically diverse sample of 50 recent modern humans and 30 chimpanzee specimens belonging to Pan troglodytes troglodytes and P. t. verus. Our measurement protocol can be applied to CT scans of different spatial resolutions because it primarily quantifies the midline skeleton of the bony labyrinth. Accurately locating the lumen centre of the semicircular canals and the cochlea is not affected by the partial volume and thresholding effects that can make the comparison of the outer border problematic. After virtually extracting the bony labyrinth from CT scans of the temporal bone, we computed its midline skeleton by thinning the encased volume. On the resulting medial axes of the semicircular canals and cochlea we placed a sequence of semilandmarks. After Procrustes superimposition, the shape coordinates were analysed using multivariate statistics. We found statistically significant shape differences between humans and chimpanzees which corroborate previous analyses of the labyrinth based on traditional measurements. As the geometric relationship among the semilandmark coordinates was preserved throughout the analysis, we were able to quantify and visualize even small-scale shape differences. Notably, our approach made it possible to detect and visualize subtle, yet statistically significant (P = 0.009), differences between two chimpanzee subspecies in the shape of their semicircular canals. The ability to discriminate labyrinth shape at the subspecies level demonstrates that the approach presented here has great potential in future taxonomic studies of fossil specimens.