Background: Fosamax, an oral bisphosphonate, is the most commonly prescribed drug for the treatment of various bones diseases. However, Fosamax therapy is associated with gastrointestinal toxicity that influences the treatment compliance. Nigella sativa (N sativa) is an annual herbaceous plant and have been safely used as a natural remedy in Egypt. It has a wide range of pharmacological activities and a proposed role in combating many gastrointestinal disorders. Aim: This work aimed to study the effect of Fosamax on the histological structure of the duodenal mucosa of albino rats and to evaluate the possible protective role of nigella sativa oil. Materials and methods: Forty adult male albino rats were divided into four equal groups: the control group, the N sativa oil-treated group (2.5 ml/kg), the Fosamax-treated group (0.05mg/kg), and both Fosamax and N sativa oil-treated group. Treatments were given orally once weekly for 13 weeks. Specimens from the duodenum were processed for light microscopy. Immunohistochemical study was carried out using antibodies against nuclear factor-κB (NF-κB), cyclooxygenase-2 (COX-2), B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax) and Ki67 protein. Results: Specimens from Fosamax-treated rats showed a statistically significant decrease in the duodenal mucosal thickness. The lining epithelium showed nuclear alteration and vacuolated cytoplasm and there was mononuclear cellular infiltration. The immunohistochemical study of Fosamax-treated group showed a significant increase in NF-kB, COX-2 and Bax immunoreaction and a significant decrease in Bcl-2 and Ki67 expression. In contrast, minimal changes were observed in rats treated concomitantly with both Fosamax and N sativa oil with non-significant changes in the immunoreactions compared with the control group. Conclusion: Fosamax induced structural changes in the duodenal mucosa of adult albino rats, which could be ameliorated by concomitant treatment with nigella sativa oil.