The direct synthesis of hydroxyapatite (HA)-aspartic acid (ASP) and HA-glutamic acid (GLU) nanocrystals was carried out in presence of different amounts of the amino acids in solution. ASP and GLU incorporation into HA crystals reduces the coherent length of the perfect crystalline domains along the long dimension (002) and, even more, along the cross section (310) of the apatite crystals, suggesting a specific interaction of the amino acids with the HA structure. FTIR analysis indicates that the carboxylic groups of the acidic amino acids interact with the calcium ions of HA. The relative amount of ASP incorporation into HA nanocrystals is greater than that of GLU, suggesting a greater affinity of ASP for HA. Osteoblast-like, MG63, cells cultured on the composite nanocrystals display good proliferation and increased values of ALP activity, collagen type I, TGF-betaI and osteocalcin production, indicating that the presence of the acidic amino acids enhances osteoblast activation and extra-cellular matrix mineralization processes.