Malignant mesothelioma is a tumour originating from mesothelial cells, and it exhibits epithelial, fibrous, or biphasic differentiation. This tumour is highly resistant to therapy, and presence of a sarcomatous growth pattern has been associated with worse prognosis. A mesothelioma cell line with retained ability to differentiate into either epithelial or fibroblast-like phenotype was subjected to subtractive hybridisation in order to identify the genes coupled to tumour cell differentiation. Nine genes were found to be selectively overexpressed in the epithelial sub-line, compared to only two genes in the fibroblast-like phenotype. This may support the idea that the sarcomatous phenotype represents a less differentiated tumour. One of the genes that is differentially expressed by the epithelial cells was thioredoxin, a small redox-active protein associated with cell-growth and differentiation. This overexpression was accompanied by increased protein levels both intracellularly and in the medium. Thioredoxin is reduced by the selenoprotein thioredoxin reductase and NADPH. The activity of this enzyme was high in both cell sub-lines but induced 2-fold in the epithelially-differentiated cells. Overexpression of thioredoxin might be a factor behind the poor prognosis and reduced responsiveness to therapy of mesotheliomas. Epithelial differentiation in this cell line has previously been linked to increased synthesis of heparan sulphate proteoglycans. The possible formation of complexes including thioredoxin, thioredoxin reductase, and heparan sulphate proteoglycans might play a role in the local control of cell growth and differentiation.