Interleukin 4 (IL-4) has an indispensable role in the differentiation of naive T helper (Th) cells toward the Th2 phenotype and induction of B cells to produce the IgE class of Igs. By regulating these two cell types, IL-4 has a pre-eminent role in regulation of allergic inflammation. IL-4-mediated regulation of T and B cell functions is largely transmitted through signal transducer and activator of transcription 6 (Stat6). In this study, we have used metabolic labeling and 2-D electrophoresis to detect differences in the proteomes of IL-4 stimulated spleen mononuclear cells of Stat6-/- and wild type mice and MS/MS for protein identification. With this methodology, we identified 49 unique proteins from 21 protein spots to be differentially expressed. Interestingly, in Stat6-/- CD4(+) cells the expression of isoform 2 of core binding factor b (CBFb2) was enhanced. CBFb is a non-DNA binding cofactor for the Runx family of transcription factors, which have been implicated in regulation of Th cell differentiation. We also found cellular nucleic acid protein (CNBP) to be downregulated in Stat6-/- cells. None of the proteins identified in this study have previously been reported to be regulated via Stat6. The results highlight the importance of exploiting proteomics tools to complement the studies on Stat6 target genes identified through transcriptional profiling.