Abstract: Objective: To explore the prognostic factors affecting the survival of patients with malignant thymoma. Methods: A total of 72 patients with malignant thymoma surgically treated from June 1994 to June 2003 were studied retrospectively. The possible prognostic factors were analyzed by univariate analysis and multi-variate analysis with Kaplan-Meier, Log-rank and Cox proportional hazard model. Results: Overall patients survival rates were 74.08%、55.60%、44.66% at 1, 3, 5 years, respectively. The significant prognostic factors demonstrated by univariate analysis included incision, invasion of great blood vessels, Masaoka staging and WHO histologic classification (P<0.05). According to multivariate analysis, the independent prognostic factors were invasion of great blood vessels, Masaoka staging and WHO histologic classification. Conclusion: Surgical resection is the effective treatment of malignant thymoma. Howerer, innvasion of great blood vessels, Masaoka staging and WHO histologic classification are the independent pognostic factors of those patients.