The aim of the present study was to analyze the expression of S100A4 and E-cadherin in a panel of primary and metastatic malignant melanoma, and to correlate the expression level to clinicopathological parameters. The expression of S100A4 was examined by immunohistochemistry in 99 superficial spreading and 60 nodular primary melanomas, while the expression of E-cadherin was analyzed in 92 superficial spreading and 52 nodular lesions from the same panel. The expression levels of S100A4 and E-cadherin in the biopsies were inversely correlated, with S100A4 being expressed at the highest frequency in the nodular and E-cadherin in the superficial spreading lesions, respectively. When analyzing the melanoma subgroups separately, it was revealed that expression of S100A4 had a more significant impact on patient outcome in early superficial spreading melanomas than in the nodular subtype, while E-cadherin expression did not predict patient outcome in any of the subgroups. When examining all the patients, both markers give clinical information as predictors for disease-free survival, but when combining the expression of the two markers, a stronger significant correlation between high E-cadherin expressing/S100A4 negative biopsies and increased disease-free survival (P=0.002) was revealed, demonstrating the importance of examining the expression of more than one factor involved in the metastatic cascade when predicting patient outcome. We have also evaluated the relationship between the expression of these two antigens and cell cycle and signal transduction factors.