Discrete dental traits are used as proxies for biological relatedness among modern human populations and for alpha taxonomy and phylogeny reconstruction within the hominin clade. We present a comparison of the expression of lower molar dental traits (cusp 6, cusp 7, trigonid crest pattern, and protostylid) at the enamel-dentine junction (EDJ) in a variety of extant and fossil hominoid taxa, in order to assess the contribution of the EDJ to the morphology of these traits at the outer enamel surface (OES). Molars (n=44) were imaged nondestructively using high-resolution microCT, and three-dimensional surface models of the EDJ and OES were created to compare trait expression at each surface. Our results indicate that these dental traits originate at the EDJ, and that the EDJ is primarily responsible for their degree of expression at the OES. Importantly, variable trait morphology at the EDJ (often not easily recognizable at the OES) indicates that different developmental processes can produce traits that appear similar at the enamel surface, suggesting caution in intra- and intertaxonomic comparisons. The results also highlight the importance of the EDJ for understanding the morphological development of discrete traits, and for establishing graded scales of variation to compare trait frequency among groups for the purpose of taxonomic and/or phylogenetic analysis. Finally, this study demonstrates that imaging the EDJ of both worn and unworn fossil hominin teeth provides a novel source of information about tooth development and variation in crown morphology.