The degradation reaction of thermally treated 3-deoxy-d-erythro-hexos-2-ulose and methylglyoxal, both key intermediates in Maillard chemistry, was investigated. Different analytical strategies were accomplished to cover the broad range of formed products and their different chemical behavior. These involved HPLC-DAD and accordingly LC/MS analysis of the quinoxaline derivates, GC/MS analysis of the acetylated quinoxalines, and GC-FID analysis of the decyl ester of acetic acid. As a main degradation product of 3-deoxy-d-erythro-hexos-2-ulose, 5-(hydroxymethyl)furfural could be identified. At alkaline pH values, 3-deoxy-d-erythro-hexos-2-ulose generated various acids but no colored products. In contrast, thermal treatment of methylglyoxal yielded high molecular weight, brownish products. A dimer of methylglyoxal, first precursor for aldol-based polymerization of methylglyoxal, could be clearly identified by GC/MS.