The aim of this study was to characterize the physico-chemical properties and bone repair after implantation of zinc-containing nanostructured porous hydroxyapatite scaffold (nZnHA) in rabbits' calvaria. nZnHA powder containing 2% wt/wt zinc and stoichiometric nanostructured porous hydroxyapatite (nHA - control group) were shaped into disc (8 mm) and calcined at 550 °C. Two surgical defects were created in the calvaria of six rabbits (nZnHA and nHA). After 12 weeks, the animals were euthanized and the grafted area was removed, fixed in 10% formalin with 0.1 M phosphate buffered saline and embedded in paraffin (n=10) for histomorphometric evaluation. In addition, one sample from each group (n=2) was embedded in methylmethacrylate for the SEM and EDS analyses. The thermal treatment transformed the nZnHA disc into a biphasic implant composed of Zn-containing HA and Zn-containing β-tricalcium phosphate (ZnHA/βZnTCP). The XRD patterns for the nHA disc were highly crystalline compared to the ZnHA disc. Histological analysis revealed that both materials were biologically compatible and promoted osteoconduction. X-ray fluorescence and MEV-EDS of nZnHA confirmed zinc in the samples. Histomorphometric evaluation revealed the presence of new bone formation in both frameworks but without statistically significant differences (p>0.05), based on the Wilcoxon test. The current study confirmed that both biomaterials improve bone repair, are biocompatible and osteoconductive, and that zinc (2wt%) did not increase the bone repair. Additional in vivo studies are required to investigate the effect of doping hydroxyapatite with a higher Zn concentration.