Proteolysis in cheese is confirmed as a major event during ripening, of significance for both texture and flavour of the final product. In this report the crude fractionation methods described previously have been grouped into schemes that should facilitate the laboratory work. Each scheme contains the necessary fractions to describe cheese proteolysis at different levels of significance for the main proteolytic and peptidolytic activities in cheese. The work done in the area of capillary electrophoresis is reviewed. The effective use of high performance liquid chromatography (HPLC) in showing the characteristic profiles resulting from different activities in cheese is dealt with. Finally, the advantages and disadvantages of currently used methods to analyse amino acids in cheese are discussed.