Molar enamel thickness is a key feature in the study of hominid evolution. Our understanding of enamel thickness and distribution patterns, however, has so far been based mostly on the limited information available from physical cross sections of the crown. In this study, the 3-dimensional (3D) whole crown enamel distribution pattern was explored in 74 extant great ape and modern human molars. Serial cross sections obtained from microfocal X-ray computed tomography were used to generate digital molar reconstructions at 50 to 80 micron voxel resolution, each crown represented by two to five million voxels. Surface data of both enamel dentine junction (EDJ) and outer enamel were extracted to derive volumetric measures, surface areas, curvilinear distances, and whole crown radial thickness maps. Three-dimensional average enamel thickness (AET) was defined as enamel volume divided by EDJ surface area. In 3D AET relative to tooth size, Homo exhibited the thickest, Gorilla the thinnest, and Pan and Pongo intermediately thick enamel. This result differs from previous claims that molar enamel of Pongo is relatively thicker than that of Pan. The discrepancy between three and two-dimensional (2D) values of AET stems from a combination of local differences in within tooth enamel distribution pattern and EDJ topography between Pan and Pongo molars. It demonstrates that 2D AET is not an appropriate substitute or estimator of whole crown AET. Examination of whole crown 3D distributions of molar enamel revealed a pattern common to all four examined species, the “functional” side of the molar having thicker enamel than the opposite side. However, some unique aspects of each species were also apparent. While the Gorilla molar has relatively thin enamel throughout its crown, Pan molars are characterized by particularly thin enamel in the occlusal fovea, and Pongo molars by an accentuation of relatively thin basal and thick occlusal enamel. Human molars are characterized by relatively thick enamel throughout the crown, with relatively large contrasts between buccal and lingual, and between mesial and distal crown portions. The ancestral condition common to the four extant species can be estimated by interpreting molar enamel distribution patterns unique to each genus as likely to be derived. We hypothesize that the last common ancestor likely had intermediately thick enamel, without particular thickening (or thinning) of enamel either occlusally or basally.