This study investigated the interactions of reactive alpha-dicarbonyl compounds, particularly methylglyoxal (MGO) and 3-deoxyglucosone (3-DG), in commercial biscuits during gastrointestinal digestion. An in vitro multi-step enzymatic digestion system simulating gastric, duodenal and colon phases was used. MGO and 3-DG concentrations decreased with the progress of digestion. Model systems composed of MGO and lysine, cysteine or ovalbumin and model biscuits containing lysine, cysteine or ovalbumin were subjected to in vitro digestion. The results revealed that disappearance in dicarbonyl contents was due to interactions of reactive dicarbonyl compounds with the accumulating amino acids during digestive process. By a high resolution mass spectrometry analysis in model systems and biscuits, the formation of adducts of dicarbonyl compounds with amino or sulfhydryl groups of amino acids was confirmed.