In this study we evaluated the existing association between naturally occurring subclinical intramammary infection, in combination with somatic cell count, with the detailed protein profile in Holstein cows assessed at the individual quarter level. We observed that the infection, but mostly the inflammation status of the mammary gland, affected the milk protein profile, and in particular the casein fractions. These results helped elucidate the behavior of protein fractions during subclinical intramammary infection.