The prognosis of thymic epithelial tumours depends on malignant behaviour that cannot always be predicted on histological grounds. This study aimed at identifying a molecular marker that would be useful in overcoming the drawbacks of histopathology. Forty-four thymic epithelial tumours were analysed for alterations of the tumour suppressor gene p53 using immunohistochemistry (antibodies D0-1 and CM-1) and PCR-based single-strand conformation polymorphism and DNA sequencing. Histological and clinical evaluation and also p53 analysis revealed three major tumour groups: non-organotypic thymic carcinomas with frequent p53 alterations (7/9) and occurrence of p53 gene mutations (2/9); malignant thymomas with frequent p53 alterations but without p53 gene mutations (11/18); and benign thymomas with rare p53 alterations and without p53 gene mutations (2/17). In non-organotypic thymic carcinomas p53 was detected with both antibodies. In contrast, thymomas lacked immunoreaction with D0-1 suggesting alteration of the antibody-binding site. Overall immunohistochemical results correlated with clinical stages (P < 0.01), pathohistology (P < 0.01), and survival times (P < 0.05). We consider immunohistochemical p53 detection to be a useful new prognostic factor for the evaluation of thymic epithelial tumours.