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The aim of this study was to compare a second-generation bioactive glass putty biomaterial against platelet rich fibrin in treating grade II furcation defects. Subjects were 15 systemically healthy patients (10 males and 5 females, ages 20-50 with a mean age of 38.33) with 20 mandibular molar class II furcation defects according to Glickman's classification. The 20 mandibular molar furcation defects were randomly allocated as follows: Group I, 10 furcation defects were treated using bioactive glass (NovaBone) bone graft putty material; Group II, 10 furcation defects were treated using platelet rich fibrin (PRF). Customized acrylic stents were fabricated on study casts and trimmed to the height contour of the teeth to serve as a fixed reference point for measurements. The following measurements were collected: gingival index, plaque index, vertical probing depth (from gingival margin to base of the pocket), clinical attachment level (CEJ to the base of the pocket), and horizontal probing depth of furcation involvement (using stent). Results showed that both groups had improvement in gingival index (GI) and plaque index (PI) at the recall intervals. There was an overall reduction in both vertical and horizontal probing depth in both groups; however, the Putty group (Group I) showed consistently more vertical probing depth reduction than the PRF group (Group II) at the end of third month (P-value = 0.0004), sixth month (P-value = 0.00001), and ninth month (P-value = 0.0004). Our conclusion was that use of bioactive glass osteostimulative biomaterial yields superior clinical results, including increased pocket depth reduction of class II furcation defects as compared to an autologous platelet concentrate. The clinical significance of our findings include the ease of use and superior biologic performance of second-generation putty bioglass biomaterials in furcation defects.