Bisphosphonates are commonly used in clinical practice. Their effectiveness is indisputable, however their adverse effects, especially in the GI tract, are still controversial. In our report, we demonstrate pathological findings of the effect of systematic alendronate administration in esophagus, stomach and the liver of an in-vivo animal model of 15 Wistar rats. Light microscopy with immunohistochemistry and electron microscopy were used. Microscopic findings of inflammation of the stomach and mild hepatic dysfunction were observed. Conclusively, alendronate can potentially affect gastric mucosa and liver function on this animal experimental model.