Abstract We and others have shown that dipeptidyl peptidase-4 (DPP4) promotes inflammation in a number of conditions. However, it’s role in inflammatory colitis is not fully understood. Here we examined the role of DPP4 in dextran sulfate sodium (DSS)-induced colitis model and T cell transfer model of chronic colitis. The expression of DPP4 was significantly decreased in the colon tissue of wild-type (WT) mice with colitis. The mortality and disease activity score were markedly increased in mice deficient for DPP4 (Dpp4−/−), compared to WT mice. Chimeric mice with Dpp4−/− bone marrow showed a similar disease severity to whole body DPP4 knockout mice in DSS induced colitis, suggesting that bone marrow-derived immune cells were responsible for the protective effect of DPP4 on colitis. Flow cytometry analysis indicated that DPP4 was mainly expressed in T cells and dendritic cells (DCs) in mesenteric lymph nodes. Using T cell transfer model of chronic colitis in Rag2−/− mice or Dpp4−/− Rag2−/− mice, we found that innate immune cells other than adaptive immune cells were responsible for the protective effect of DPP4. Subsequent flow cytometric analysis showed that DPP4 was mainly expressed on a DC subset that was responsible for the induction of regulatory T cells (Tregs) in the gut. RNA sequencing data also indicated that expression of genes in TGFβ signaling pathway was significantly reduced in Dpp4−/− mice, accompanied by an increased expression of multiple inflammatory genes. Co-transfer of WT Tregs protected Rag2−/− mice, but not Dpp4−/− Rag2−/− mice, from developing colitis after transfer of CD4+ naive T cells. Our data suggest that DPP4 expression on innate immune cells may be responsible for maintaining Treg’s suppressive function in colitis.