CD25⁺CD4⁺ regulatory T cells have major roles in controlling immune responses, and use heterogeneous regulatory mechanisms. It is possible that these different activities aremediated by different subsets. Here we show that CD103⁺CD25⁺CD4⁺ T cells (that control inflammatory bowel disease) are highly enriched in gut‐associated lymphoid tissue and have unique functional properties. In vivo, only this subpopulation is able to control wasting disease and peripheral T cell homeostasis. In vitro, only this subpopulation is able to regulate IL‐10 secretion, and it might also mediate infectious suppression. These results demonstrate that regulatory T cells can be divided into discrete subpopulations with defined functional properties and regulatory mechanisms.