The human selenoenzyme thioredoxin reductase 1 (TrxR1) is a very important enzyme for cell growth, differentiation, and the defense against oxidative stress. Several studies have shown that TrxR1 is up-regulated in tumor cells. The regulation of TrxR1 is very complex and involves the expression of different transcript forms of mRNA. We have, by quantitative polymerase chain reaction, investigated the total expression of TrxR1 mRNA and quantified the expression of alternative mRNA forms (alpha1/2, alpha6, alpha7/8, alpha10/11, alpha13, gamma2-4, and beta1) in six different human malignant mesothelioma cell lines of epithelioid, sarcomatoid, or mixed phenotype. The most abundant alpha-form was surprisingly alpha1/2 and not the expected alpha7/8. Selenium treatment resulted in increased expression of all alpha-variants, except the alpha10/11, where the levels were unaffected. The expression of protein isoforms was studied and the less abundant forms TrxR1v.2, TrxR1v.3, and TrxR1v.5 were detected in cell lysates and in human tumor tissue, using specific peptide antibodies. Furthermore, TrxR1v.3 and TrxR1v.5, previously not identified in human cells, were detected by mass spectrometry. Our data show differential expression of TrxR1 mRNA forms in malignant mesothelioma of different phenotype, and investigation of alternative transcript variants of TrxR1 could be a valuable tool in the diagnostics and characterization of tumors.