During the last decade, research into genetic markers in the casein gene cluster has been actively introduced in cattle breeding programs. A special interest has been paid to the polymorphism of theCSN3gene, responsible for the expression of the k-casein, playing a key role in protein coagulation, interaction with whey proteins, stabilization, and aggregation of casein micelles. This paper aimed to determine the effect ofCSN3genetic polymorphism on acid; rennet; acid–rennet; heat- and acid-induced as well as heat- and calcium-induced coagulation in skimmed milk; and protein-standardized milk systems (UF, NF, RO, VE). The influence of polymorphic variants of theCSN3gene on the coagulation ability of milk proteins was assessed by the particle size of casein micelles, protein retention factor in the clot, and coagulation ability (duration of induction period, mass coagulation period, dynamic viscosity in gel point). The correlation betweenCSN3gene polymorphism and protein coagulation was revealed. Milk systems obtained fromCSN3 BBmilk were found to have the shortest duration of coagulation, formation of better gel strength values, and increased yield compared toCSN3 AA. This study will improve the efficiency of milk processing and optimize the technology of dairy product production.