Milk is a complex biological fluid that ensures the correct growth and development of young mammals. Depending on the stage of lactation, milk is classified as colostrum secreted three days post-parturition and milk produced 72 h after the delivery and they have slightly different nutrient and protein composition. It was shown that the proteome of bovine milk is represented by over 4500 different proteins. In the present paper by using a gene ontology analysis (String analysis), proteins identified in bovine colostrum and milk were grouped into two categories: proteins involved in immunological processes and proteins associated with digestive system development. Among these proteins, proteins characteristic to either colostrum or milk were identified, among others kininogen-2 and cathepsin L1. The constant development of proteomic techniques leads to the identification of novel cow’s whey proteins that have not been found yet. The new, low- and medium-abundant proteins help to better understand the physiological process of calf growth and maturation.