We have evaluated whether cyclosporine A affects cell structure and cytoskeletal proteins of the thymus of Wistar rats. Immunohistochemical analysis showed that expression of the cytoskeletal proteins vimentin and desmin was much higher in epithelial cells, dendritic cells and lymphocytes in the thymus of treated rats than in untreated controls. Protein expression was observed as a positive condensation in a distinct area near the nucleus with a capping-like configuration. An ultrastructural study showed that the amount of cytoskeletal fibrillar structures was increased in the treated rats. The structures were assembled in a limited area of the cell with a nuclear capping-like configuration which was in agreement with the light microscopical observations. Immunoblotting analysis demonstrated that vimentin and desmin had a lower molecular weight in treated rats than in controls (57 and 53 kDa versus 55 and 51 kDa, respectively). The results clearly indicate that cyclosporine A affects the structure of the cytoskeleton suggesting that this could be the first step in its immunosuppressive effects by altering nucleus/cytoplasm signaling.