Bats exhibit remarkable diversity in dietary habits, with species specializing on insects, fruit, nectar, vertebrates and blood. Studies of larger mammals have shown that structural differences in dentary cross-sectional properties exist among species with different diets. Unfortunately, few of these studies have considered the role of phylogeny in shaping these apparent form-function associations. Here we ask whether a relationship exists between diet and dentary structure in bats when phylogenetic history is factored into the analysis. To answer this question, we compared results from phylogenetic generalized least squares (PGLS) and traditional (nonphylogenetic) regression analyses of dentary cross-sectional shape in frugivorous, nectarivorous, and insectivorous bats (253 individuals representing 72 species). Cross-sectional moments of inertia of the dentary between M(1) and M(2) were computed from bone densitometry scans of skeletal specimens. Traditional regressions of cross-sectional parameters against dentary length detected significant departures from isometry among frugivores. In contrast, PGLS analyses indicated that cross-sectional variables for each dietary group scaled with isometry. Thus, the allometric patterns illuminated by traditional statistics are linked to the phylogenetic structure of the sample. Identical patterns of significant differences in slopes and intercepts between frugivores and nectarivores emerged from both traditional and PGLS analyses. As predicted, the cross-sectional shape of the dentary in frugivores is consistent with increased resistance to torsion and bending, while that of nectarivores suggested a less resistant dentary. Although traditional and PGLS analyses yielded some similar results, the phylogenetic structure of a sample can drive apparent patterns of scaling and should be considered in comparative functional analyses.