Depending on whether milk protein fractions are evaluated qualitatively or quantitatively, different genetic outcomes may emerge. In this study, we compared the genetic parameters for the major milk protein fractions-caseins (αS1-, αS2-, β-, and к-CN), and whey proteins (β-lactoglobulin, β-LG; α-lactalbumin, α-LA)-estimated using the multi-trait genomic best linear unbiased prediction method and expressed variously as milk content (g/100g milk), percentage of milk nitrogen (%N) and daily yield per cow (g/d). The results showed that the genetic parameter estimates varied according to how the milk protein fractions were expressed. Heritability estimates for the caseins and whey protein fractions expressed as daily yields were lower than when they were expressed as proportions and contents, revealing important differences in genetic outcomes. The proportion and the content of β-CN were negatively correlated with the proportions and contents of αS1-CN, αS2-CN, and к-CN, while the daily yield of β-CN was negatively correlated with the daily yields of αS1-CN and αS2-CN. The Spearman's rank correlations and the coincidence rates between the various predicted genomic breeding values (GEBV) for the milk protein fractions expressed in different ways indicated that these differences had a significant effect on the ranking of the animals. The results suggest that the way milk protein fractions are expressed has implications for breeding programs aimed at improving milk nutritional and technological characteristics.