Milk protein is an important component of the human diet throughout much of the world. The ability to assess the relative composition and integrity of milk proteins or peptides in dairy foods or food ingredients is important because these molecules have a profound effect on product functionality and quality. This communication describes two capillary electrophoretic methods that are useful for the analysis of proteins and casein-derived peptides in cheese and milk products. One technique, which uses a buffer containing citrate/phosphate (pH 3.3), 4 M urea, and a polymeric additive in a coated capillary, is useful for qualitative and quantitative analysis of proteins and peptides in milk, cheese, and whey products. The second method employs a citrate/phosphate buffer (pH 2.8) and a bare silica capillary, and is well suited for the analysis of small, casein-derived peptides in aqueous cheese extracts.