The mechanical properties of bone depend largely on its degree and distribution of mineralization. The present study analyzes the effect of an inhomogeneous distribution of mineralization on the stress and strain distributions in the human mandibular condyle during static clenching. A condyle was scanned with a micro-CT scanner to create a finite element model. For every voxel the degree of mineralization (DMB) was determined from the micro-CT scan. The Young's moduli of the elements were calculated from the DMB using constant, linear, and cubic relations, respectively. Stresses, strains, and displacements in cortical and trabecular bone, as well as the condylar deformation (extension along the antero-posterion axis) and compliance were compared. Over 90% of the bone mineral was located in the cortical bone. The DMB showed large variations in both cortical bone (mean:​ 884, SD:​ 111 mg/cm3) and trabecular bone (mean:​ 738, SD:​ 101 mg/cm3). Variations of the stresses and the strains were small in cortical bone, but large in trabecular bone. In the cortical bone an inhomogeneous mineral distribution increased the stresses and the strains. In the trabecular bone, however, it decreased the stresses and increased the strains. Furthermore, the condylar compliance remained relatively constant, but the condylar deformation doubled. It was concluded that neglect of the inhomogeneity of the mineral distribution results in a large underestimation of the stresses and strains of possibly more than 50%. The stiffness of trabecular bone strongly influences the condylar deformation. Vice versa, the condylar deformation largely determines the magnitude of the strains in the trabecular bone.