There is a bidirectional relationship between autoimmunity and cancer: on the one hand, patients with autoimmune conditions develop neoplastic diseases, and on the other hand, malignant conditions are associated with paraneoplastic autoimmune syndromes. Thymoma is an epithelial tumor which is often accompanied by autoimmune diseases: about a third of the patients with thymoma have myasthenia gravis. Pure red cell aplasia, pemphigus and systemic lupus erythematosus, might also coexist with this tumor. Thymectomy is an optional treatment in some autoimmune diseases (i.e. myasthenia gravis, multiple sclerosis, autoimmune hemolytic anemia, ulcerative colitis, and systemic lupus erythematosus). In this communication we review and discuss the coexistence of autoimmune diseases, thymoma or thymic hyperplasia, and the dual effects of thymectomy on their course.