Coagulating properties of milk have influence on cheese-making ability, cheese yield, and its quality. The aim of this study was to find the effects of major milk proteins contents and their genetic variants on milk rennet coagulation properties in Estonian dairy breeds. During the years 2001-2005 a total of 1,269 cows were on repeated occasions sampled (n = 8,282). Higher contents of milk protein, total casein, the casein number, and alpha(S1)-, beta-, and kappa-Cn, and beta-Lg, reduced the rennet coagulation time and formed a firmer curd. A higher proportion of kappa-Cn with respect to alpha(S1)-Cn and beta-Cn assisted in forming a firmer curd. All measured rennet coagulation parameters were significantly better for the kappa-Cn BB, and worse for the kappa-Cn AA, AE, and EE genotypes. Noncoagulated milk originated mainly from cows possessing kappa-Cn AA genotype. Better milk coagulation properties among ER and EN cows, compared to EHF cows, are explainable by a higher frequency of the kappa-casein B allele, associated with better coagulation properties, and ER cows also recorded higher contents of milk proteins, compared to EHF cows.