The thymus is a central lymphatic organ that is responsible for many immunological functions, including the production of mature, functional T cells and the induction of self-tolerance. Benign or malignant tumors may originate from the thymus gland, with thymoma being the most common and accounting for 50% of anterior mediastinal tumors. Malignancies linked to thymoma include the loss of self-tolerance and the presence of autoimmunity. In this review, we compiled the current scientific evidence detailing the various interactions between thymoma and autoimmune diseases, including myasthenia gravis, systemic lupus erythematosus, inappropriate antidiuretic hormone secretion, pure red cell aplasia, pernicious anemia, pemphigus and autoimmune thyroid diseases. In recent years, several mechanisms have been proposed to explain these interactions. Most are based on the assumption that the 'sick' thymus, like the 'normal' thymus, can generate mature T cells; however, the T cells generated by the sick thymus are impaired and thus may exert cellular autoreactivity. Here, we present several theories that may shed light on the loss of self-tolerance associated with this epithelial tumor of the thymus.