A decrease in casein number (i.e. the content of casein in relation to total protein) in milk during the last 30 years, as reported by the Swedish Dairy Association, may be related to an increasing milk production. The objective of this investigation was to study the relations between whey protein composition and daily milk yield using proteomics combined with multivariate data analysis. The results indicated that several individual minor whey proteins increased with increasing milk yield. Some of these proteins could be identified by mass spectrometry, including: fatty acid binding protein, apolipoprotein A1, lactoferrin and endopin. The technique used proved to be a useful tool for identification of significant proteins extracted from large data sets.