Much attention has been focused on the role of mechanical stimuli in bone remodeling because of the clinical needs for bone prostheses and fracture healing. However, little is known about the alterations of bone architecture related to mechanical environments. In this study, rat caudal vertebrae were subjected to daily cyclic loading regime. In order to reveal the influences of morphological alterations and new bone formation to the stress distribution, we estimated Von Mises stresses with three-dimensional finite element (FE) models constructed from micro-CT structural measurements. FE analyses indicated that woven bone formation over periosteum distributed stress concentration caused by external loading. Von Mises stresses in the offset loaded rat distributed uniformly under the analytical offset loading condition. Changes of tissue stress distribution related to adaptive remodeling could be predicted qualitatively by using image-based three-dimensional FE analysis.