Preferential alignment of biological apatite (BAp) crystallites seems closely related to the bone mechanical function due to the crystallographic anisotropy of its hexagonal structure. BAp alignment as well as bone shape and bone mineral density (BMD) is therefore one of the important factors for understanding the recovery of microstructure and mechanical properties in regenerated bones. A rabbit osteotomy model was examined to investigate the recovery process of defected bones. After the introduction of a 10 mm long segmental defect in mature rabbit ulnae, the bone defect was healed spontaneously for 4 and 20 weeks. To evaluate the original and regenerated hard tissues, BMD and BAp alignment along the longitudinal direction were analyzed using peripheral quantitative computed tomography (pQCT) and microbeam X-ray diffractometer system, respectively. Four weeks after the operation, the regenerated tissue showed quite a lower degree of BAp alignment than the intact original tissue; it showed no preferential BAp alignment center in the (002) pole figure. In this stage, the regenerated new bone was hardly subjected to loading. At 20 weeks, in contrast, BMD was restored to almost original levels, and the BAp alignment of the regenerated new bone depended strongly on its position under loading conditions. The regenerated degree of BAp preferential alignment showed a high correlation (R2 = 0.85) with the local stress component proportionally expressed by the reciprocal value of the ulnar cross-sectional area. Recovery of BAp alignment of regenerated bones was finally concluded to depend on the stress component in vivo along the longitudinal direction after BMD restoration.