CD69 is highly expressed by lymphocytes at mucosal surfaces, but its role in immune responses is largely unknown. I aimed to investigate the role of CD69 in mucosal immune responses. The expression of CD69 by spleen, mesenteric lymph nodes, small intestinal and colonic lamina propria CD4 T cells was determined in specific pathogen free B6 and T cell receptor (TCR) transgenic mice and in germ-free B6 mice and intestinal microflora depleted TCR transgenic animals. Colitis was induced by transplanting RAG-/- mice with B6, CD69-/- or type I interferon receptor (IFNAR)-deficient CD45RBhigh CD4 T cells or by dextran sodium sulphate (DSS) treatment. CD69 expression by CD4 T cells is induced by the intestinal microflora, oral delivery of specific antigen or type I interfrons. CD69-/- CD4 T cells produce increased amounts of pro-inflammatory cytokines IFN-gamma, TNF-alpha and IL-21 and decreased amounts of regulatory cytokine TGF-ß1. Furthermore, CD69-deficient CD4 T cells show reduced potential to differentiate into Foxp3+ regulatory cells (Treg) in vivo and in vitro. The transfer of CD69-/- CD4 T cells into RAG-/- hosts or DSS administration to CD69-/- mice induce an accelerated colitis. CD69-/- CD4 T cells express higher levels of chemokine ligands and receptors and migrate more efficiently to the intestinal tissues in vivo compared to B6 cells. Oral tolerance is impaired in CD69-/- and IFNAR-/- mice comparing to B6 and OT-II x RAG-/- animals. Polyinosine polycytidylic acid (poly (I:C)) treatment of RAG-/- mice transplanted with B6 but not CD69-/- or IFNAR-/- CD4 T cells attenuate transfer colitis. In the line with this, CD69 deficiency on CD4 T cells affected poly (I:C)-induced IFN-ß1 expression. CD69 deficiency led to the increased production of pro-inflammatory cytokines and chemokines, reduced Foxp3+ Treg cell induction, impaired oral tolerance and more severe colitis. Hence, the activation antigen CD69 plays an important role in regulating mucosal immune responses