Protein oxidation in milk products may entail flavor changes through reactions at methionine residues. However, little is known about the extent of methionine oxidation in milk and milk products. In the present study, a method for quantitation of methionine, methionine sulfoxide, and methionine sulfone by a stable isotope dilution assay using HILIC-ESI-MS/MS was established. For the quantitation of protein-bound analytes, anaerobic enzymatic hydrolysis was optimized to suppress artificial methionine oxidation. Moreover, the method allowed for monitoring of artificial oxidation by coincubation of the labeled probe [²H₈]methionine. The percentage of oxidized methionine was low in UHT milk (up to 1.6%) and evaporated milk (up to 8.8%), but higher in beverages such as cocoa milk drinks (up to 19.0%) and coffee milk drinks (up to 32.8%), resulting in methionine sulfoxide concentrations of up to 6.7 g/kg protein in the latter. These products are important dietary sources of methionine sulfoxide. Model studies revealed that methionine residues can be oxidized strongly in the presence of phenolic compounds such as catechin, caffeic acid, and gallic acid, which are present in cocoa and coffee and may account for the high extent of oxidation in commercial samples.