A method recently described for the separation of denatured α-, β- and κ-caseins by hydrophobic interaction chromatography was validated by the analysis of reference skim milk powder (BCR-063R) certificated for total nitrogen content. The method is based on fast and easy solubilization of commercial and real samples by 4.0 M guanidine thiocyanate and elution on a TSK-Gel® Phenyl-5PW column (TosoHaas) in the presence of 8.0 M urea in the mobile phase. No preliminary precipitation or separation of the casein fraction is required. A linear relationship between the concentration of casein and peak area (UV absorbance detector at 280 nm) was obtained over the concentration range 0.5–60 μM. The detection limits for α-, β- and κ-caseins ranged between 0.30 and 0.65 μM. The precision of the method was evaluated; the relative standard deviation for α-, β- and κ-casein determination ranged between 2.2 and 2.7% for standard solutions and between 3.5 and 6.2% for real sample solutions. The mean casein content found in 10 aliquots of BCR-063R calculated with respect to the total protein content (estimated on the basis of certified total nitrogen content) was 79.1 ± 2.7%. Results of linear fitting of standard additions data for α-, β- and κ-caseins to BCR-063R were compared with linear fitting of α-, β- and κ-casein calibration data. The method was applied to commercial caseins and to 31 real, raw samples [processed cow’s milk (pasteurised, UHT-treated), follow-up milk powders, cream, cheeses, casein-free infant formulae, cookies for babies containing milk proteins] with the aim of showing the wide applicability of the method in order to determine α-, β- and κ-caseins.