Introduction: Platelet rich fibrin is a concentrated suspension of growth factors, which is used to promote periodontal tissue regeneration. Hydroxyapatite (HA) permit outgrowth of osteogenic cells from existing bone areas to fill the furcation defects. The aim of the present study was to clinically and radiographically evaluate the efficacy of autogenous bone graft combined with autologous platelet rich fibrin (PRF) (Group I) and Hydroxyapatite bone graft combined with autologous platelet rich fibrin (Group II) in augmenting the bone fill of Grade II furcation defects in Mandibular molars. Materials and Methods: A total of 30 patients with Grade II furcation defects in mandibular molars were divided into Group I, treated with autogenous bone graft combined with autologous platelet rich fibrin and Group II with Hydroxyapatite combined with autologous platelet rich fibrin after ethical clearance. At baseline and 6 months after treatment, Vertical Probing Depth (VPD) Vertical Depth of The Furcation Defect (V1, V2) Horizontal Probing Depth of Furcation Defect(H1,H2) Clinical attachment level (CAL) were evaluated. Results: The mean value of the amount of furcation defect fill after 6 months using 1x1mm grid RVG is 5.06±0.89mm (P<0.001) in autogenous bone graft combined with autologous platelet rich fibrin (Group I) and 3.93 ± 0.70mm (P<0.001) in Hydroxyapatite combined with autologous platelet rich fibrin (Group II). With statistically significant bone fill in group I. Conclusion: Autogenous bone grafts with PRF have better regenerative potential than hydroxyapatite bone graft with PRF in class II furcation defects in Mandibular molar region.