Disruption of mucosal immunity plays a critical role in the pathogenesis of inflammatory bowel disease, yet its mechanism remains not fully elucidated. Here, we found that activating transcription factor 3 (ATF3) protects against colitis by regulating follicular helper T (T FH ) cells in the gut. The expression of ATF3 in CD4 + T cells was negatively correlated with the severity of ulcerative colitis in clinical patients. Mice with ATF3 deficiency in CD4 + T cells (CD4 cre Atf3 fl/fl ) were much more susceptible to dextran sulfate sodium-induced colitis. The frequencies of T FH cells, not other T cell subsets, were dramatically decreased in Peyer's patches from CD4 cre Atf3 fl/fl mice compared with Atf3 fl/fl littermate controls. The defective T FH cells significantly diminished germinal center formation and IgA production in the gut. Importantly, adoptive transfer of T FH or IgA + B cells caused significant remission of colitis in CD4 cre Atf3 fl/fl mice, indicating the T FH -IgA axis mediated the effect of ATF3 on gut homeostasis. Mechanistically, B cell lymphoma 6 was identified as a direct transcriptional target of ATF3 in CD4 + T cells. In summary, we demonstrated ATF3 as a regulator of T FH cells in the gut, which may represent a potential immunotherapeutic target in colitis.activating transcription factor 3 | follicular helper T cell | Peyer's patches | intestinal mucosal immunity | colitis