The sphenoid is often considered to be the keystone of the skull. Many cranial traits are used to distinguish phylogenetic groups among primates, and the sphenoid is an influential element in these differences. Because of the importance of the sphenoid for the integration of face, vault, and cranial base, we expected that many of these traits would be apparent early in cranial osteogenesis, establishing the framework for future development. We tested three specific hypotheses in neonate specimens of haplorhine and strepsirrhine primates. First, based on greater encephalization of haplorhine adult primates relative to strepsirrhine primates (and despite reports that haplorhines show pronounced brain growth postnatally), we predicted that the cranial base would show greater flexion in haplorhines. Second, based on expanded temporal lobes in haplorhines relative to strepsirrhines, we expected that the alisphenoid would be expanded in haplorhines. Third, based on orbital convergence of haplorhine adult primates, we predicted that the width of the presphenoid would be greater in strepsirrhine neonate primates relative to haplorhines.We evaluated perinatal (late fetal through six days postnatal) specimens of primates representing strepsirrhine and haplorhine taxa. MicroCT imaging data were used to create 3D reconstructions of each cranium. Cranial base angle was estimated by the angle between the sphenoidal and clival planes. The alisphenoid was evaluated qualitatively as the rostral portion of that bone separating orbit and middle cranial fossa. Finally, width of the presphenoid was evaluated as the width between the optic canals, inferior to the orbitosphenoid (lesser wings).Our results indicate that the sphenoid is highly variable in structure among the primate taxa under study. In all cases, the intrasphenoidal synchondrosis between the presphenoid and the basisphenoid remained patent. In many cases, the alisphenoid elements remained separate. We observed notable variation in the presphenoid, including length and width of the lesser wings. Despite the apparent variation, we did not find consistent evidence in support of our expectations based on phylogenetic signal. Cranial base angle did not differ between haplorhines and strepsirrhines, indicating that the influence of encephalization affects the cranial base postnatally. This is consistent with reports of increased brain growth in haplorhines in the postnatal period. We observed an expanded alisphenoid in haplorhines relative to some, but not all, of the strepsirrhines. Notably, the strepsirrhine Otolemur showed alisphenoid expansion rostral to the poles of the temporal lobes. Finally, we found a relatively wide presphenoid in many, but not all, of the strepsirrhines. The lesser wings of the presphenoid accommodated an enlarged olfactory fossa in all strepsirrhines, but the relative width of the presphenoid of Otolemur was within the range observed in haplorhines. Our results indicate that some of the sphenoidal traits that carry a phylogenetic signal in adults are present in many, but not all, neonate primates. These include width of the presphenoid and extent of the alisphenoid. In contrast, the effect of encephalization on cranial base angle occurs postnatally. In addition, it is apparent that factors independent of phylogeny influence the structure of the sphenoid in neonate primates.Support or Funding InformationNSF BCS‐1231717, NSF BCS‐1231350, NSF BCS‐0959438