Since preferential orientation of c-axis of biological apatite (BAp) crystallites depends strongly on the shape of hard tissue, closely relating to the in vivo stress distribution, it is a useful parameter to judge the bone quality. In this study, preferential alignment of BAp crystallites in original and regenerated hard tissues were analyzed by the micro-beam X-ray diffractometer (μ-XRD) with a beam spot of 50 or 100 μm in diameter. Regenerating processes of bone defects introduced artificially in the rabbit ulna or skull were healed by inserting a biodegradable gelatin hydrogel incorporating basic fibroblast growth factor-2 (FGF-2). Recovery of BAp orientation alignment depends strongly on the regenerated portion and period, which is insufficient to recover the original level, while bone mineral density (BMD) is almost improved to the original level. This means that BMD recovers prior to improvement of the BAp orientation and the related mechanical function in the regenerated tissues. Thus, reloading on the regenerated portion caused by BMD restoration is suggested to accelerate to produce the appropriate BAp preferential alignment due to the remodeling process. The BAp orientation was finally concluded to be one of the most important indices to check the regenerative degree and process in the regenerated bone under the tissue engineering technique.