MUC1 is a transmembrane mucin that has been related to tumor progression and outcome in various malignancies. However, the clinical significance in thymic epithelial tumors remains unknown. We investigated the clinical significance of MUC1 expression in thymic epithelial tumors. Fifty-five patients with thymic epithelial tumors were included in this study. Tumors sections were stained by immunohistochemistry for MUC1, vascular endothelial growth factor (VEGF), microvessel density (MVD) determined by CD34, and p53. MUC1 were expressed in 29%. The expression of MUC1 was significantly correlated with the grade of malignancy in thymic epithelial tumors. MUC1 was closely associated with VEGF, p53 and MVD, and the overexpression of MUC1 was a prognostic marker for predicting poor outcome in univariate analysis. A positive rate of MUC1 expression was 94% (16/17) in thymic carcinomas and 0% (0/5) in type B3 thymomas, demonstrating a significant difference (p < 0.0001). The expression of MUC1 was closely related to the grade of malignancy in thymic epithelial tumors. A positive expression of MUC1 was significantly associated with poor outcome in this disease. MUC1 may be useful marker for differentiating thymic carcinoma from type B3 thymoma.