SDS-PAGE (sodium dodecyl sulphate – polyacrylamide gel electrophoresis) was used as preliminary analysis of whey proteins of raw, commercial pasteurized and commercial ultra-high temperature (UHT) milks. Four whey proteins bands, including β-lactoglobulin variants (β-LG A and B), could be distinctively separated in the gel. The results showed that levels of the major whey proteins were reduced in the pasteurized milks and UHT milks as compared with raw milk. Peptides of bovine milk were separated further on by two-dimensional gel electrophoresis (2-D electrophoresis, 2-DE). The peptides were separated in the pH range 3-10 in the first dimension, while 12%T homogenous gels were used in the second dimension. 2-D electrophoresis analysis of UHT milk sample showed a decrease in the number of proteins and peptides.