The linked IL-4 and IL-13 cytokine genes, which are activated and silenced in T helper (Th) 2 and Th1 cells, respectively, are flanked by the equivalently expressed RAD50 and KIF3A genes. A scan of DNase I hypersensitivity and DNA methylation across approximately 100 kb of the KIF3A/IL-4/IL-13/RAD50 cluster revealed differences in chromatin structure between Th1 and Th2 cells at the 3' end of the RAD50 gene, a region previously shown to contain a locus control region (LCR) regulating Th2-specific expression of IL-4 and IL-13. Naive CD4 T cells did not exhibit any DNase I hypersensitivity in this region, but stimulation under either Th1 or Th2 conditions caused rapid development of three hypersensitive sites. An additional hypersensitive site developed rapidly only under Th2 conditions, through a mechanism dependent on signal transducers and activators of transcription 6 (STAT6) but not GATA3. Our data point to a physical separation in the actions of STAT6 and its downstream effector GATA3 during Th2 differentiation: STAT6 directly remodels the RAD50 LCR, whereas GATA3 acts only in the vicinity of the IL-4 gene. We suggest that the RAD50 LCR has a complex and dual role in Th1 and Th2 differentiation, communicating early T cell antigen receptor and cytokine signals to the IL-4/IL-13 locus in both differentiating cell types.