Bioactive peptides have proven to be active in several conditions, including inflammatory bowel disease (IBD). This is a chronic and relapsing condition of unknown aetiology that comprises chiefly ulcerative colitis and Crohn's disease. Although there are treatments for IBD, they have frequent side effects and they are not always effective; therefore there is a need for new therapies that could alleviate this condition. Two bioactive peptides present in milk (transforming growth factor-β (TGF-β) and casein macropeptide, also named glycomacropeptide) have been shown to have intestinal anti-inflammatory activities. In fact, TGF-β is currently added to formulas intended for patients with IBD, and several studies indicate that these formulas could induce clinical remission. In this paper, evidence supporting the anti-inflammatory effect of TGF-β and bovine glycomacropeptide, as well as their mechanisms of action, is reviewed, focusing on the evidence obtained in animal models.