Proteomics, an innovative branch of science, deals with comprehensive analysis of protein expression at a particular time in a given biological system. Proteomics enables analysis of the repertoire of proteins, comparison of protein profiles, and reveals changes in expression. Proteomic studies may be useful in solving scientific problems and may have applications in practice. The use of proteomic techniques is increasing in relation to farm animals in order to assess their health status, growth rate and productivity, but it is worth emphasizing that still is inadequate to needs. The detection of biomarkers enables early diagnosis, prevention, and finding therapeutic solutions. During puberty in heifers and during the first pregnancy and lactation, dynamic and gradual adaptive changes in the intensity of metabolic processes and changes in the activity of regulatory mechanisms are observed. These changes are associated with the growth and development of the foetus, preparation of the mammary glands for lactation, and, after parturition, with reproductive system regeneration and preparation for new fertilization and pregnancy. Comparison of protein profiles and identification of differentially expressed proteins involved in particular metabolic pathways may be useful in comprehensive analysis of functional changes in pregnant and lactating cows. Current knowledge, results of scientific studies, and their application into practice indicate that proteomics will introduce new standards into physiological research in the near future. This paper presents studies on pregnant and lactating cows, with emphasis on proteomics of blood serum/ plasma, foetal membranes, liver, amniotic fluid, allantoic fluid, uterine fluid, urine, mammary gland, milk, and comparative proteomics of healthy and sick cows.