Combining in situ tailing and immunocytochemical staining, we demonstrated that the infiltrating macrophages in muscle tissue sections during early phase of experimental autoimmune myasthenia gravis (EAMG) in Lewis rats were eliminated by apoptosis at high frequency. These apoptotic macrophages were colocalized in the end-plate regions. Apoptosis is a major cause for elimination of infiltrating macrophages during the early phase of EAMG.