This paper presents a comprehensive comparative analysis of the Neanderthal bony labyrinth, a structure located inside the petrous temporal bone. Fifteen Neanderthal specimens are compared with a Holocene human sample, as well as with a small number of European Middle Pleistocene hominins, and early anatomically modern and European Upper Palaeolithic humans. Compared with Holocene humans the bony labyrinth of Neanderthals can be characterized by an anterior semicircular canal arc which is smaller in absolute and relative size, is relatively narrow, and shows more torsion. The posterior semicircular canal arc is smaller in absolute and relative size as well, it is more circular in shape, and is positioned more inferiorly relative to the lateral canal plane. The lateral semicircular canal arc is absolutely and relatively larger. Finally, the Neanderthal ampullar line is more vertically inclined relative to the planar orientation of the lateral canal. The European Upper Palaeolithic and early modern humans are most similar, although not fully identical to Holocene humans in labyrinthine morphology. The European Middle Pleistocene hominins show the typical semicircular canal morphology of Neanderthals, with the exception of the arc shape and inferiorly position of the posterior canal and the strongly inclined ampullar line. The marked difference between the labyrinths of Neanderthals and modern humans can be used to assess the phylogenetic affinities of fragmentary temporal bone fossils. However, this application is limited by a degree of overlap between the morphologies. The typical shape of the Neanderthal labyrinth appears to mirror aspects of the surrounding petrous pyramid, and both may follow from the phylogenetic impact of Neanderthal brain morphology moulding the shape of the posterior cranial fossa. The functionally important arc sizes of the Neanderthal semicircular canals may reflect a pattern of head movements different from that of modern humans, possibly related to aspects of locomotor behaviour and the kinematic properties of their head and neck.