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OBJECTIVE To evaluate the prognostic significance of p53, Ki-67, epithelial cadherin (E-cadherin) and matrix metalloproteinase-9 in primary penile cancer, as the presence of lymph node metastasis and long-term survival are hard to define in penile squamous cell carcinoma. PATIENTS AND METHODS Paraffin-embedded primary tumour samples were obtained from 73 Chinese patients who had penile amputation and regional lymphadenectomy. The expression of molecular markers was determined by immunohistochemistry. Logistic regression was used to identify factors associated with lymph node metastasis, and a Cox proportional-hazards model was used to measure cancer-specific survival (CSS). RESULTS Thirty (41%) patients presented with nodal disease and the 3-year CSS rate for all patients was 72%. Lymph node metastasis was significantly correlated with tumour stage, histological grade, lymphatic and vascular embolization, and the expression of p53, Ki-67 and E-cadherin. By multivariate analysis, tumour embolization and the expression of p53 were independent predictors of metastasis. Survival analysis showed that the expression of p53 was an independent prognostic factor for CSS. In stage T1 tumours, high expression of p53 was significantly associated with metastasis and poor survival. CONCLUSION Lymphatic and vascular embolization, and p53 immunoreactivity, are helpful in establishing the probability of lymph node metastasis. The expression of p53 is an independent predictor of CSS in Chinese patients with penile cancer. In stage T1 tumours, p53 staining is an important variable determining the prognosis and treatment outcome. [ABSTRACT FROM AUTHOR]