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At the nanoscale bone is composed of aligned mineralized collagen fibrils organized into packets along the surface of trabecular bone creating an anisotropic tissue microstructure. Newer packets at the trabecular surfaces are usually less mineralized than older bone in the interior of the trabeculae, which along with irregular mineral deposition within packets, forms a heterogeneous material across the span of a trabeculae. However, finite element (FE) models of bone typically use homogenous isotropic material properties, because it is challenging to build anisotropy and heterogeneity into a model in a way that is applicable to the complex geometries of trabecular bone. Both the material anisotropy and heterogeneity may influence the stress state of trabecular bone, and it is important to understand the implications of such differences for determining bone biomechanical failure. It was hypothesized that taking into consideration both the tissue anisotropy and heterogeneity of bone’s biomechanical properties would alter the expected failure locations by reducing tensile stress on near surface elements of an FE model of canine trabecular bone. The objective of this study was to test this hypothesis and to develop a method to apply anisotropic and heterogeneous material properties to a model automatically from micro-computed tomography (μCT) data.