The late Miocene hominoids Hispanopithecus from Spain and Rudapithecus from Hungary are considered to be closely related great apes (Hominidae), but uncertainties persist regarding their taxonomic distinction and exact phylogenetic placement (stem hominids vs. stem hominines). Previous studies have detected a strong phylogenetic signal in the vestibular apparatus morphology among primates. Here we use deformation-based geometric morphometrics to assess the morphological affinities of the vestibular apparatus in Hispanopithecus laietanus (IPS18000) and Rudapithecus hungaricus (RUD77 and RUD200) among a large sample of extant catarrhines. We use between-group principal components analyses (bgPCA) to explore the position of the fossils in the vestibular 3D morphospace and phylogenetic comparative methods to reconstruct its evolution. Our results indicate that hylobatids display a rather monkeylike morphology, whereas great apes clearly occupy a distinct portion of the morphospace. Our bgPCA results reflect a strong phylogenetic signal and confirm that Hispanopithecus and Rudapithecus exhibit a hominid-like morphology (thick semicircular canals, small anterior and lateral ones), their differences being compatible with the distinction of two genera. Along the first two axes of variation, and under different phylogenetic assumptions, Rudapithecus more closely approaches the reconstructed ancestral states for hominines and hominids as a whole, whereas Hispanopithecus appears more similar to orangutans (due to the possession of rather stout semicircular canals and a craniocaudally compressed anterior canal). Although formal cladistic analyses would be required to test whether these similarities are pongine synapomorphies or hominid symplesiomorphies, our study confirms the potential of vestibular morphology for phylogenetic reconstruction between fossil and extant apes.