T helper cells (Th) are divided into Th1 and Th2 subsets based upon their cytokine profiles and function. Naïve Th cells differentiate into Th1 and Th2 subsets depending on the antigens, costimulatory molecules, and cytokines they encounter. Cytokine interleukin (IL)-12 enhances the generation of Th1 lymphocytes and inhibits the production of Th2 subset. Many genes involved in Th cell differentiation have already been identified at transcriptomic level in microarray studies. In this study, isotope coded affinity tag labeling combined with chromatographic techniques and tandem mass spectrometry was used to find IL-12 regulated proteins in the microsomal fraction of Th cells. A total of 380 and 275 proteins were initially identified and quantitated in two experiments. After the high-confidence protein identifications were restricted to those where at least two different peptides were identified per protein, and these confirmed by manual inspection of the tandem mass spectra, 147 proteins remained. Of these high-confidence protein identifications 41 had at least 1.5-fold change in expression between IL-12 treated and nontreated cells. Among the differentially regulated proteins were galectin-1 (gal-1) and CD7, and their down-regulation was further corroborated with Western blotting and flow cytometry, respectively. Gal-1 and CD7 are known to interact with each other, and regulate immunity through influencing apoptosis and cytokine production. Our data indicate that IL-12 down-regulates the expression of both gal-1 and CD7 in the microsomal fraction of peripheral blood mononuclear cells and cord blood CD4(+) cells. The down-regulation of these proteins is likely to have a role in specific Th cell selection and cytokine environment creation.