Cross-linking enzymes such as transglutaminase, laccase, tyrosinase and peroxidase catalyse the formation of new covalent bonds between proteins and therefore lead to their polymerisation. This approach has been studied extensively as a way to modify physical and textural properties of (fermented) dairy products, or to create well-defined micro- and nanostructures from milk proteins that could serve as techno-functional additives in foods or as nanocarriers for molecules with nutritional benefits. This chapter gives an overview of the most prominent cross-linking enzymes in dairy science and technology, as well as approaches that are commonly applied for the analysis of cross-linking reactions and the resulting protein structures. Finally, different applications of cross-linking enzymes for milk protein modification are discussed.