Indirubin could significantly decrease DAI score and histological score of colitis mice.TNF-α, IFN-γ, IL-2, and MPO levels were decreased, and IL-10 level were increased by indirubin.The infiltration of CD4+ T cells were suppressed, and the formation of Foxp3+ expressing T cells were promoted by indirubin. This evidence concerns the gene FOXP3 and colitis.