Primate evolutionary studies rely significantly on dental variation given the large role that teeth play in how an organism interacts with its environment (animal and plant) and conspecifics. Variation in cusp size has been shown to vary among primate taxa, although most studies to date focused on extant and extinct hominoids. Here we test the assumed hypothesis that a significant proportion of this variation in baboons is due to the additive effects of genes. We perform quantitative genetic analyses on variation in two-dimensional (2-D) mandibular molar cusp size in a captive pedigreed breeding population of baboons (Papio hamadryas) from the Southwest National Primate Research Center. These analyses show that variation in cusp size is heritable and sexually dimorphic. Additionally, we tested for genetic correlations between cusps on the same crown, between morphological homologues along the tooth row, and between cusp area and crown buccolingual width. We find that four of the six cusp pairs on the first molar have a genetic correlation of one, save for the metaconid–hypoconid and entoconid–hypoconid, which are not statistically different from zero. The second and third molars have lower genetic correlations, although the metaconid–hypoconid correlation is similarly estimated at zero and the entoconid–protoconid correlation is estimated to be one. This cross pattern of genetic and no genetic correlation does not immediately accord with the known pattern of development and/or calcification. We propose two explanative hypotheses. Am J Phys Anthropol, 2007. © 2006 Wiley-Liss, Inc.