CD25(+)CD4(+) regulatory T cells have major roles in controlling immune responses, and use heterogeneous regulatory mechanisms. It is possible that these different activities are mediated 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.