Aim: This study was designed to evaluate the efficacy of 1% alendronate gel as an adjunctive therapy to scaling and root planing in the treatment of class II furcation defects. Subjects and method: Twenty-six patients with mandibular class II furcation involvement were selected from the out-patient clinic, Oral Medicine and Periodontology Department, Faculty of Dentistry, Al-Azhar University, Assiut Branch. They were divided into two equal groups. Group I received conventional periodontal therapy alone, while group II received conventional periodontal therapy combined with intra-furcal application of 1% alendronate gel as adjunctive therapy. All patients were evaluated clinically, radiographically as well as for RANKL level in GCF at base line, 3 and 6 months. Results: Both groups showed a high significant difference between base line and 6 months in all clinical parameters (PI, GI, VPD, CAL and HPD), radiographic parameters (bone density) and RANKL level in GCF. There was a statistical significant difference to group II when compared to group I in VPD and HPD at 6 months only and in CAL, bone density and RANKL level at 3 and 6 months. Conclusion: intra-furcal application of 1%Alendronate gel seemed an attractive effect as adjunctive therapy in improving the clinical, radiographic parameters and RANKL level in GCF in the treatment of class II furcation defects