Background: Bony defects caused by periodontitis are often treated by regenerative therapy using bone and bone substitutes. Alloplasts, such as hydroxy apatite is used as osteoconductive materials that serve as a scaffold for new bony ingrowth. Alloplasts composed of nano-HA have been extensively used for bone grafting procedures and have been found to be compatible with host tissues and elicits no adverse reactions.Aim of the study: Since it is hypothesized that with the nanotechnology; nano-HA might be more advantageous in regenerative therapy; The aim of the present study was to evaluate the outcome of using two different bone grafts (nanocrystalline hydroxyapatite and xenograft) with bioresorbable membrane in periodontal regenerative therapy, utilizing the use of Cone Beam Volume Tomography. Patients and methods: 20 contralateral intraosseous defects in ten medically free patients were divided randomly to receive xenograft and membrane or nano-HA and membrane. Six months postoperatively, plaque index (PI), gingival index (GI), probing pocket depth (PPD) and clinical attachment level (CAL) were recorded and compared with the baseline findings as well as the radiographic features of bone density that were evaluated using cone beam volume tomography.Results: Both treatment modalities resulted in improvement in all clinical parameters when baseline was compared to 6 months postoperatively. The results showed that Nano-HA graft with collagen membrane provided high significant differences in all clinical measures when compared to xenobone graft with collagen membrane. Regarding CBVT measurements, when bone fill was compared in each group at baseline and 6 months postoperatively, high significant difference was found in nano-HA with collagen membrane treated group than in xenobone graft with collagen membrane treated group. Conclusions: From the results of the current study we can conclude that recent developments in nanomaterials and nanotechnology have provided a promising insight into the commercial applications of nanomaterials in the management of periodontal diseases.