||Hydroxyapatite (HA) is the most important bioceramic material for hard tissue replacement in human bodies. Recently, cation substituted HA has been a research focus in order to further enhance HA bioactivity and to adapt various application requirements. Magnesium and zinc are potentially the elements to partially substitute calcium in the HA for improving osteointegration, because Mg and Zn are the most important minor and trace elements respectively in human hard tissues. Magnesium depletion affects all stages of skeletal metabolism adversely, causing cessation of bone growth, decreasing osteoblastic and osteoclastic activity, osteopenia, and bone fragility. Zn can promote bone metabolism and growth, increase bone density and prevent bone loss. Mg, Zn substitutions in the crystal structure of HA are expected to have excellent biocompatibility and biological properties. Previous researches showed no direct evidence to prove that Zn/Mg successfully substituted partial Ca in the apatite lattice but not just absorbed on the apatite surface. The apatite structural changes after substitution even the maximum amount of Mg and Zn substitution for Ca are still in controversy. Nanocrystalline Mg, Zn substituted HA particles with various Mg and Zn substitution amount were synthesized by wet chemical method. Diffraction, spectroscopy, microscopy characterization techniques were employed to investigate the substituted apatites. Especially the X-ray diffraction Rietveld Refinement method was used to examine the effects of Mg and Zn substitution on crystal structure changes. Experimental results showed that Mg, Zn successfully substituted Ca in HA. The substitution limit was between 15~20 at. % Zn and different new phases presented over this limit. While Mg substitution was rather limited (less than 5 at.%)，various non apatite phases came out when the Mg/(Mg+Ca) atomic ratio was over 15 at. % in aqueous solution. Both Zn and Mg increased the resistance of HA crystallization. After substitution, the crystallite size and crystallinity decreased. Pure HA was well crystallized and in regular shape. With the substitution content increasing, crystallites were smaller, shorter, more irregular and formed serious agglomerates. Also both Mg and Zn substitution destabilized the apatite structure and reduced the decomposition temperature of HA. The lattice parameters a and c decreased up to 10at. % in solution and then started to slightly increase.