BACKGROUND Malignant thymomas are rare neoplasms. Factors affecting prognosis and survival of patients with this neoplasm have been intensively discussed, but the results vary among different studies. To find possible prognostic factors, we designed this retrospective study. METHODS Forty-four cases of malignant thymomas diagnosed and treated in Chang Gung Memorial Hospital, Kaohsiung, from 1986 to 1996 were reviewed. RESULTS Of the 44 cases, 24 were male and 20 were female (M:F = 1.2:1). Patient age ranged from 25 to 73 years (median 48 years). Thirty-four cases (77%) belonged to type I malignant thymoma (invasive thymoma) and 10 cases (23%) belonged to type II malignant thymomas (thymic carcinoma). The most frequent histologic type was predominantly epithelial (43%), followed by mixed lymphoepithelial (27%). Six patients had myasthenia gravis. Eleven (25%) patients, including 4 cases of invasive thymoma and 7 cases of thymic carcinoma, showed tumor metastasis to lung, bone, liver, spleen and omentum. The 5-year survival was 73% for patients who underwent total tumor excision and 18% for those who received partial tumor excision or biopsy only. The influence of histologic types on prognosis is not statistically significant (P = 0.434). CONCLUSIONS Completeness of tumor excision at initial operation is the most important prognostic factor. Predominantly epithelial and mixed lymphoepithelial types are more aggressive forms with a higher tendency to invasion.