This study assessed genetically based differences in intrinsic material properties of both cortical and cancellous bone in adult females of three inbred mouse strains [C57BL/6J (B6), DBA/2J (D2), C3H/HeJ (C3)]. These mouse strains have previously been shown to differ in bone mineral content (BMC) and density (BMD). Distal femoral cancellous bone and midshaft cortical bone in femurs and tibias were assessed for intrinsic material properties using nanoindentation technique. The intrinsic material properties tested were modulus (E(b)) and hardness (H) of the midshaft femoral and tibial cortical bone cross sections and of cancellous bone in the distal femur. Both femoral and tibial cortical bone intrinsic material properties were different among the three inbred mouse strains. Femoral modulus and tibial hardness in cortical bone and hardness in cancellous bone were either greatest or showed greater trends in C3 mice as compared to both D2 and B6. Cancellous bone modulus was similar among the three mouse strains. With the exception of the D2 mice, the femoral and tibial cortical modulus were similar within each mouse strain. The tibial cortical modulus was smaller than the femoral cortical modulus for D2 mouse strain. The cortical hardness was greater in tibiae compared with that in femora within each mouse strain. The nanoindentation data suggest that cortical and cancellous intrinsic material properties are influenced by the genetic background of the inbred mouse strains. The inbred mouse strain-related intrinsic material property phenotype can be used to locate responsible quantitative trait loci (QTLs) in future studies of recombinant inbred mouse strains.