In this study, Zn incorporated non-stoichiometric hydroxyapatite (nHAp) was synthesized via precipitation method and effect of the incorporation of Zn (fraction: 2, 4, 6 and 8 mol-%) on the microstructure of nHAp was studied by XRD, FTIR analysis and SEM-EDS techniques. The formation of nHAp was confirmed by XRD and FTIR those showed that no secondary phase was formed through the Zn incorporation. The SEM studies also revealed that particles were formed in nano-metric size (30-60 nm). It was found that crystallite and particle size of Zn incorporated nHAp gradually decreased up to 6 mol-%, and started to increase while the Zn fraction reached up to the 8 mol-% and hence the morphology of the aggregated products was also changed. It can be concluded that the incorporation of Zn cations cause to form nHAp phase. Furthermore, the nHAp microstructure has deviated from stoichiometric condition by incorporation of more Zn cations.