Background The effect of bisphosphonates on the resorption process of normal bone tissue has been clearly mentioned in the literature, while their effect on the grafting material is a new research area. Limited former study is not sufficient to determine the strength, reliability and dosage of bisphosphonates. In this study, our aim is to examine the effects of local and systemic use of bisphosphonates in bone graft applications on bone healing, histopathologically. Methods Therefore, 32 Sprague-Dawley rats are separated into four groups. In the first group, only an empty bone defect is made on tibia and the tissue is sutured primarily without any other application. In the second group, bone defect is filled with allograft material and closed without any other application. In the third group (LA), alendronate solution is locally added to the graft material before its application to the site of bone defect. In the fourth group, alendronate is applied systemically after the site of bone defect is grafted and primarily closed. After 6 weeks, all rats are killed and the obtained samples are examined histopathologically. Results Local and systemic application of alendronate increases new bone formation in a statistically significant degree. In LA group, newly formed bone was observed more mature and well developed. Alendronate application does not cause an increase in inflammation, fibrosis and necrosis. There is no increased necrosis with alendronate application. Conclusion Local and systemic application of alendronate in bone grafting increases bone formation without any other complication. But we believe that further research should be made on dosage, usage and possible side effects.