Most recent phylogenetic analyses place the Cainotheriidae within the Tylopoda, but doubts about this placement within Tylopoda have been persistent. The Cainotheriidae are well known from numerous specimens and their cranial anatomy is well documented from complete, partial and disarticulated cranial material. However, high-resolution computed tomographic (CT) scans can still provide additional data to resolve problems in the interpretation of the auditory region, and allow comparison with other tylopod and ruminant taxa. Cainotheriids share several features with various groups within the Tylopoda, including an enlarged mastoid fossa, an inflated auditory bulla filled with cancellous bone, the presence of a sinus venosus temporalis, and what has been interpreted as a large flange of the periotic enclosing the petrobasilar canal. The reconstruction of the petrobasilar canal has been difficult to interpret, as the published figures are unclear. A micro-CT scan of Cainotherium (YPM 25037) shows the morphology is more complex. The periotic shows a smaller flange that does not enclose the petrobasilar canal. The skull base shows different arrangement of bones from other artiodactyls, presumably as a result of the enlargement of the auditory bulla, which has also affected the course of the petrobasilar canal. The otic region of Cainotherium shows no resemblances to ruminants, and features of this region are consistent with the Cainotheriidae being either a sister taxon to Tylopoda Ruminantia, or with inclusion in a tylopod grouping.