Background: To evaluate the relative efficacy of synthetic nanocrystalline hydroxyapatite (HA) (Ostim®) and microcrystalline HA (Osteogen®) bone grafts in the treatment of human periodontal intrabony defects clinically and radiographically through denta scan. Materials and Methods: Ten chronic periodontitis patients with bilateral intrabony periodontal defects of ≥2 mm radiographic defect depth below 55 years of age were selected randomly and treated with synthetic nanocrystalline HA (Ostim®) or synthetic microcrystalline HA (Osteogen®) bone graft. Clinical parameters including probing depth (PD) and clinical attachment level (CAL) were measured preoperatively and postoperatively at 3 and 6 months for each of the defects using an occlusal acrylic stent. Radiographic parameters were measured with the help of denta scan preoperatively and postoperatively at 6 months. Results: At 6 months following therapy, the Osteogen® group showed a reduction in mean PD from 11.10 ± 1.663 to 8.50 ± 0.850 mm and a change in mean CAL from 6.30 ± 1.160 to 3.40 ± 0.516 mm, whereas in the Ostim® group, the mean PD decreased from 11.20 ± 0.919 to 8.30 ± 0.823 mm and mean CAL decreased from 6.10 ± 0.738 to 3.30 ± 0.483 mm. At 6 months following therapy, denta scan showed a reduction in mean intrabony defect depth in the Osteogen® group from 2.54 ± 0.786 to 1.01 ± 0.448 mm, whereas in the Ostim® group, it was 2.71 ± 0.650 mm to 1.12 ± 0.563 mm. Conclusion: It was concluded that both the HA bone grafts produced statistically significant reduction in pocket depth, in the depth of osseous lesion, and a statistically significant gain in attachment level, irrespective of their physico-chemical properties.