Objective: Background: This study evaluated the clinical and microbiological efficacy of Alendronate (ALN) gel versus Chlorohexidine (CHX) gel as an adjunct to mechanical therapy in the treatment of chronic periodontitis and compared this effect with Scaling and Root Planning (SRP) only. Materials and Methods: Forty patients with chronic periodontitis were randomly allocated into two groups. Each group of twenty patients was split into a study group and a control group, group 1 was treated on one side with ALN gel after (SRP) and the other side was treated with (SRP) only. group 2 was treated on one side with CHX gel after (SRP) and the other side was treated with (SRP) only. Clinical parameters such as plaque index (PI), clinical attachment level (CAL), probing depth (PD), sulcus bleeding index (SBI), and microbiological assessment as total bacterial count, prevotella intermedia, porphyromonas gingivalis were evaluated after three months. Results: It has been shown that there was a significant difference in clinical and microbiological assessment for all groups when comparing pre-treatment measurements vs post-three months treatment measurements. While there was no significant difference in both clinical and microbiological assessment after three months when comparing treatment groups of alendronates after SRP vs CHX after SRP. Conclusion: Considering the clinical and microbiological relevance, local application of either ALN gel or CHX gel is considered a valid adjunctive therapy to SRP.