The whey protein nitrogen index (WPNI) is an established method for grading skim milk powder (SMP) products depending on their heating history. This method is based on the principle of salting out of denatured soluble protein (whey proteins) and then an acid-induced aggregation of the remaining native protein, which causes an increase in turbidity. The WPN index is derived from a standard curve. The objective of this research was to evaluate if WPN number is also applicable to milk protein concentrates (MPC), as in these systems, the type of soluble proteins and their aggregation state may be different than in skim milk powders, after reconstitution. WPN numbers were derived, and the composition of the serum phase as well as the level of denaturation for various milk concentrates and isolates were measured using nitrogen analysis, as well as electrophoresis and cation exchange chromatography. To test the method, milk powder products were reconstituted to a final protein content of 3.2% and skim milk was used as standard. The results show that WPN numbers obtained from the standard method were higher than the cation exchange chromatography. The denaturation of whey proteins, especially the β-lactoglobulin, was inhibited in MPC compared with SMP. In MPC 70, the WPN number obtained from cation exchange chromatography was 5.24 ± 0.12 mg/g, while the WPN number for low heat SMP was only 3.98 ± 0.11 mg/g. Therefore, the WPNI method is not an appropriate method to determine the undenatured whey proteins for MPC as their turbidity values are out of the range of the standard curve. Alternatively, the method of cation exchange chromatography exhibits great accuracy and reproducibility and can be used for determining the undenatured whey proteins in both liquid and powder milk products.