Milk contains a number of indigenous enzymes that play an important role in processing and quality of milk for direct consumption and cheese. This chapter discusses only the use of exogenous enzymes, with particular emphasis to innovative applications. To this aim, applications have been classified into three main groups: use in cheese making, applications for shelf-life extension, and applications for functional and environmental purposes. Milk coagulants belong to four main categories: animal rennet, plant-derived coagulants, microbial coagulants, and genetically engineered chymosin. The principal application of exogenous lipases in the dairy industry is enhancing cheese flavor and acceleration of cheese ripening throughout controlled hydrolysis of triglycerides. The use of antimicrobial enzymes is a natural means to control microbial contamination, improving safety and shelf life of dairy products. Most applications involve lysozyme and lactoperoxidase. Transglutaminase (TG) has recently become of great interest to food scientists for its ability in strengthening the structure of protein gels.