An analytical method was developed and validated for simultaneous identification and quantification of advanced glycation end products (AGEs), amino acid cross-links, lysine and arginine in foodstuffs based on acid hydrolysis, hydrophilic interaction chromatography and high-resolution mass spectrometry. The method proved to be sensitive, reproducible and accurate for furosine, N-Ɛ-(carboxymethyl)lysine, N-Ɛ-(carboxyethyl)lysine, methylglyoxal and glyoxal-derived hydroimidazolones (MG-H and GO-H isomers, respectively), glyoxal lysine dimer, lysinoalanine, lanthionine, lysine and arginine. LOD and LOQ values in water were found to be 0.9–15.5 ng/mL and 2.8–47 ng/mL, respectively, and increased to 1.4–60 ng/mL and 4.4–182 ng/mL in liquid infant formula. Recovery values ranged from 76 to 118% in four different food matrices. Microwave-assisted hydrolysis for 11 min had similar efficiency as conventional hydrolysis, which requires overnight incubation. Acid stability of each compound was determined during microwave and conventional hydrolysis, and showed that the MG-H1 isomer is partially converted to the MG-H3 isomer during acid hydrolysis.