The purpose of the present study was to clinically and radiographically evaluate and compare the efficacy of demineralized freeze dried bone allograft (DFDBA) and bovine derived xenogenic bone graft (BDX) [Bio-Oss] with amniotic membrane (AM) as guided tissue regeneration (GTR) in the treatment of human periodontal Grade II buccal furcation defects. Ten patients suffering from chronic periodontitis, displaying bilateral Grade II buccal furcation defect, were randomly treated using DFDBA with AM (Experimental site A) or using bovine derived xenograft (BDX) with AM (Experimental site B). The clinical and radiographic parameters were recorded at baseline, 6 and 9 months. Healing was uneventful in all patients except one site which was treated with BDX + AM. At 9 months after therapy, soft tissue measurements for the DFDBA + AM group showed pocket depth (PD) reduction of 4.7 mm +/- 0.58, and relative attachment level gain of 4.8 mm + 0.32, while the BDX + AM group showed a PD reduction of 4.4 mm +/- 0.27, and AL gain of 5.1 mm +/- 0.09. Osseous measurements showed bone fill of 2.1 mm +/- 0.36 for the DFDBA + AM group and 2.43 mm +/- 0.38 for the BDX + AM group. Percentage gain in bone was 76.3% for the DFDBA + AM group and 79.6% for the BDX + AM group. Statistical analysis revealed there was no statistical difference between the two materials in all measurements. Within the limits of the present study, it can be concluded that: (1) at 9 months after surgery both therapies resulted in significant PD reductions and CAL gains and (2) significant improvement was seen in bone fill and percentage gain with both the material, however, there was no significant difference between both.