The basicranium has been argued to contain a strong phylogenetic signal in previous analyses of primate cranial morphology. Therefore, further study of basicranial morphology may offer new insights into controversial phylogenetic relationships within primate groups. In this study, I apply 3-D geometric morphometric techniques in a phylogenetic analysis of the African papionin basicranium. The effects of allometry strongly influence African papionin basicranial morphology and, unless these size effects are controlled or eliminated, phylogenetic analyses suggest traditional phylogenetic groupings of small taxa (mangabeys) and large taxa (geladas, mandrills, drills, and baboons). When the effects of allometry are eliminated by excluding size-correlated principal components (PCs) or by regression analysis with retention of residuals, phylogenetic analyses of African papionin basicranial morphology are incongruent with recent molecular and morphological studies. By contrast, a cladistic analysis of basicranial characters using the narrow allometric coding method suggests the same phylogenetic relationships as recent molecular and morphological studies. These results suggest that important phylogenetic information is contained within the size-correlated data, and this information is being discarded during the attempt to eliminate the effects of body size. Future 3-D morphometric studies of phylogeny should focus on the development of new methodologies to adjust for allometric effects, as current techniques appear to be ill-equipped to deal with the case of a size-disparate, lower-level taxonomic group. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc.