Recent nanoindentation studies have demonstrated that the hardness and Young's modulus of human molar enamel decreases by more than 50% on moving from the occlusal surface to the dentin-enamel junction on cross-sectional samples. Possible sources of these variations are changes in local chemistry, microstructure, and prism orientation. This study investigates the latter source by performing nanoindentation tests at two different orientations relative to the hydroxyapatite prisms: parallel and perpendicular. A single sample volume was tested in order to maintain a constant chemistry and microstructure. The resulting data show very small differences between the two orientations for both hardness and Young's modulus. The 1.5 to 3.0% difference is significantly less than the standard deviations found within the data set. Thus, the variations in hardness and Young's modulus on cross-sectional samples of human molar are attributed to changes in local chemistry (varying levels of mineralization, organic matter, and water content) and changes in microstructure (varying volume fractions of inorganic crystals and organic matrix). The impact of prism orientation on mechanical properties measured by nanoindentation appears to be minimal.