A dominant inorganic substance in hard tissue is known to be a biological apatite (BAp) nano-crystal which basically crystallizes in an anisotropic hcp lattice, and the BAp c-axis is parallel to extended collagen fibrils. We applied the microbeam X-ray diffractometer system with an incident beam spot 100 mu m or 50 mu m in diameter to the original, regenerated and pathological hard tissues in order to analyze the preferential alignment of the BAp c-axis as a parameter of bone quality closely relating to the mechanical function. We conclude that the BAp orientational distribution in the hard tissues is a new measure to evaluate stress distribution in vivo, nano-scale microstructure and the related mechanical function, healing process of the regenerated bone and progress of the bone diseases.