Activation and migration of regulatory T cells (Treg) into tissue is critical in control of inflammation, but has not been examined extensively in chronic graft versus host disease (cGVHD). In parallel studies of tissues and blood, we determined that FoxP3+ T cells increased in proportion to T effectors (Teff) in tissue infiltrates in oral and cutaneous lichenoid cGVHD. These FoxP3+ cells expressed distinguishing phenotypic and functional markers of Treg (CD3+, CD4+, CD27+, ICOS+ and CD39+), not found on FoxP3− Teff. Both Teff and FoxP3+ Treg expressed T-bet and the chemokine receptor CXCR3, however, consistent with a common mechanism of chemokine-mediated migration into tissue. Furthermore, functional markers (ICOS and CD39) and chemokine receptors (CXCR3) were both present in a higher proportion of FoxP3+ cells in tissues than in peripheral blood, consistent with recruitment and activation of Treg in cGVHD target tissues. Finally, the ‘activated’CD45RA− FoxP3 hi subset of Treg cells, which highly express functional markers, were found in comparable frequencies in cGVHD patients and normal controls, despite a significant deficit in naive ‘resting’Treg. These findings are consistent with Treg capacity to upregulate functional markers and traffick into tissue in cGVHD.