The objective of this study was to evaluate the different pathological and clinical characteristics of thymomas with and without myasthenia gravis (MG) and to determine whether the presence of MG influences the prognosis in thymoma patients. We retrospectively studied data from 228 consecutive patients operated on from 1992 to 2007 in Beijing Tongren Hospital. These thymoma patients have been subdivided into two groups: group A with MG (n = 125) and group B without MG (n = 103). There were no perioperative deaths. There were 19 inoperable cases (6 in the group with MG, 13 without MG, P = 0.035). The proportions of types A, AB, B1, B2, B3, and C thymoma in this data were 0, 22.4, 26.4, 30.4, 20.8, and 0%, respectively, in the group with MG, and 10.5, 13.4, 23.6, 24.5, 16.4, and 11.6%, respectively in the group without MG. There was a significant difference between hyperplastic paraneoplastic thymus coexisting in 28.8% patients with MG and only 5.8% in patients without MG. Microthymoma was identified in the paraneoplastic thymus of three patients with MG. There were 198 patients followed up. There was no recurrence in patients with type A, and a few patients with types AB, B1, B2, B3, and C recurred. The actuarial 5- and 10-year survival rates were 89.3 and 81.2% for patients with MG, respectively, and 90 and 78.9% for patients without MG, respectively. Within 5 years postoperatively, 6 of 9 patients with MG died of myasthenia crisis, while 6 of 7 deaths in patients without MG were attributable to inoperable tumors (stage IV) and type C thymoma. MG seldom occurs in types A and C thymoma. MG of some thymoma patients was not caused by thymoma, but by the paraneoplastic thymus. The prognosis of thymomas with MG is similar to that without MG. The main cause of death is myasthenia crisis for thymoma patients with MG and stage IV and/or type C for thymoma patients without MG.