Hydroxyapatite nanoparticles were synthesized in the presence of two kinds of acidic amino acids in order to investigate the effects of acidic amino acids on the morphology of hydroxyapatite obtained by homogeneous precipitation and hydrothermal treating. The results of X-ray diffraction analysis and microphotographs of transmission electron microscope showed that the morphology of hydroxyapatite nanoparticles changed significantly only with aspartic acid. Hydroxyapatite synthesized with aspartic acid showed smooth flake-like morphology at pH= 11 and flake-like morphology with stripes at pH= 8. However, hydroxyapatite synthesized in the present of glutamic acid showed rod-like morphology at both pH values. Variation in the morphology of nanoparticles could be consistent with the difference in the affinity of amino acids binding at the hydroxyapatite crystal surface. The adsorption process was revealed by computer simulation of molecular mechanics using energy minimizing method.