Raw milk adulteration with cheese whey is a major problem that affects the dairy industry. The objective of this work was to evaluate the adulteration of raw milk with the cheese whey obtained from the coagulation process, with chymosin enzyme using casein glycomacropeptide (cGMP) as an HPLC marker. Milk proteins were precipitated with 24% TCA; with the supernatant obtained, a calibration curve was established by mixing raw milk and whey in different percentages, which were passed through a KW-802.5 Shodex molecular exclusion column. A reference signal, with a retention time of 10.8 min, was obtained for each of the different percentages of cheese whey; the higher the concentration, the higher the peak. Data analysis was adjusted to a linear regression model, with an R2 of 0.9984 and equation to predict dependent variable (cheese whey percentage in milk) values. The chromatography sample was collected and analyzed by three tests: a cGMP standard HPLC analysis, MALDI-TOF spectrometry, and immunochromatography assay. The results of these three tests confirmed the presence of the cGMP monomer in adulterated samples with whey, which was obtained from chymosin enzymatic coagulation. As a contribution to food safety, the molecular exclusion chromatography technique presented is reliable, easy to implement in a laboratory, and inexpensive, compared with other methodologies, such as electrophoresis, immunochromatography, and HPLC-MS, thus allowing for the routine quality control of milk, an important product in human nutrition.