Crystallinity of hydroxyapatite (HAp) in bioaffinitive disperse systems was increased by a wet mechanochemical treatment at room temperature. Silk fibroin (SF) and/or hyaluronic acid (HYA) were used as bioorganics. With the mechanochemical treatment, the crystallite size and the aspect ratio of HAp decreased and became closer to that of swine trabecular bone. Mechanochemical effects on the HAp nanocrystals were discussed in terms of coherent chemical interaction between HAp and bioorganics.