Digestion of proteins leads to the release of numerous peptides in the gastrointestinal tract, among them several bioactive peptides. This review compiles, organises and critically analyses the information available on bioactive peptides present in vivo in the digestive tract of adult humans and animals. It focuses on milk proteins, which are recognised as one of the main sources of bioactive peptides with different biological functions. To date, few studies have been performed on the presence of milk-derived peptides in the intestinal tract in vivo. The diversity of these studies is remarkable in terms of the milk products that have been tested, the animal models selected and the segment of the digestive tract considered. Altogether, 69 bioactive peptides identified in vivo are reviewed. Most of them are released from casein, and especially from β-casein, to which 38 bioactive peptides are attributed. These sequences can be classified mainly as angiotensin-converting enzyme (ACE) inhibitors, opioids and antimicrobial peptides. Particular attention is paid to β-casomorphins and caseinomacropeptide-derived peptides. The function of caseinophosphopeptides as a mineral carrier is also discussed. Few bioactive peptides derive from whey proteins.