The mechanical properties of bone are dictated by the size, shape and organization of the mineral and matrix phases at multiple levels of hierarchy. While much is known about structure-function relations at the macroscopic level, less is known at the nanoscale, especially for trabecular bone. In this study, high resolution transmission electron microscopy (HRTEM) was carried out to analyze shape and orientation of apatite crystals in murine femoral trabecular bone. The distribution and orientation of mineral apatites in trabecular bone were different from lamellar bone and the c-axis of the tablet-like mineral apatite crystals in trabecular bone was arranged with no preferred orientation. The difference in the orientation distribution of apatite crystals of trabecular bone in the present study compared with that of lamellar bone found in the literature can be attributed to the more complex local stress state in trabecular bone. Apatite crystals were also found to be multi-crystalline, not single crystalline, from dark field image analysis. From the observations of this study, it is suggested that Wolff's law can be applicable to the nanostructural orientation and distribution of apatite crystals in trabecular bone. It was also found that small round crystalline particles observed adjacent to collagen fibrils were similar in size and shape to the apatite crystals in biomimetically nucleated synthetic amorphous calcium phosphate, which suggests that they are bone mineral apatite nuclei.