Bovine milk contains a range of indigenous proteolytic enzymes and enzyme systems. The major bovine proteolytic enzyme in milk is plasmin (Chap. 2), being part of a complex system consisting also of proenzymes, activators and inhibitors, called the plasminogen system, coming from the blood. Other proteolytic enzymes in milk can be secreted from the somatic cells, leaked from dead cells or even secreted by mammary epithelial cells. These enzymes mainly comprise of the lysosomal cathepsins and, amongst these, cathepsin D is the most well described, but other cathepsins are also present. These indigenous proteases belong to various classes, and exhibit different specificities and requirements for activity, as well as segregate into different fractions during processing. Thereby, they can affect the yield, quality and shelf life of milk and dairy products, depending on different conditions such as their heat stability and accessibility to substrates. Indigenous proteolytic enzymes in milk for example, may contribute to lower cheese yield or contribute to instability of UHT milk. On the other hand, biologically speaking, they may have physiological roles linked to pre-digestion in the infant, formation of bioactive peptides and reorganisation of mammary tissue. In cheese, they contribute to cheese ripening by providing the larger polypeptides used further down in the process by, e.g., microbial proteases involved in cheese texture and aroma development. For all enzymes, it is important to note that there are likely differences between what is experienced in model systems using pure protein substrates (e.g., individual caseins) and what is happening in the actual dairy matrices.