An analytical high-performance liquid chromatography (HPLC)-fluorescence method for indirect measuring of whey protein in casein coprecipitate and milk powder was developed. Samples were hydrolyzed with HCl, and cysteyl residues were derivatized with 3,3'-dithiodipropionic acid and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. The cysteine content was used to calculate the percentage of whey protein in commercial samples with use of European Union Regulation cysteine reference values in both casein and whey protein. Method validation studies were performed for caseinates and milk powder, and results indicate that the present HPLC approach can be applied as a fast method with a standard deviation of repeatability between 3.3 and 9.5%. Applicability was studied by analysis of 40 commercial caseinate samples, and all complied to European legislation with a content of whey protein not exceeding 5%. Finally, an approach used to estimate the cysteine amount in pure casein by comparison of calculated and experimental values questions the generally accepted cysteine reference value in casein, which is most likely an overestimation.