Leptictis haydeni Leidy, 1868, from the early Oligocene of South Dakota is the type species of the genus and is known only from the well-preserved holotype cranium. The anatomy of its basicranium is described and illustrated based on CT scan data and the primary neurovascular structures are reconstructed. Comparisons are made with a cranium of Leptictis dakotensis (Leidy, 1868) also based on CT scan data. Numerous differences between the two are identified, including the shape of the hypophyseal fossa, the size and orientation of the posterior clinoid process, the depth of the sulcus for the capsuloparietal emissary vein, the size of the petrosal contribution to the middle cranial fossa and to the epitympanic recess, the position of the exit of the auditory tube from the middle ear, the size of the entotympanic, the presence of a styliform process on the entotympanic, and the shape of the ectopterygoid process of the alisphenoid, which added to the few prior reported dental differences justify retaining separate species. The ramus inferior of the stapedial artery, identified by prior authors as present in L. dakotensis, is shown to be absent in both species. Additional comparisons are made with the early Eocene palaeoryctid Eoryctes melanus Thewissen and Gingerich, 1989, also based on CT scans. These three taxa share details of the tympanic processes and epitympanic wings of the bones of the middle ear, the pattern of the dural sinuses and the large size of the sigmoid sinus, the well-developed exposure of the parietal on the occiput, and the unusual course of the nerve of the pterygoid canal, suggestive of a possible close phylogenetic relationship.