Oxidation of aviation fuels prior to combustion affects the safe operation of high performance aircraft. This study reports the use of comprehensive two-dimensional gas chromatography (GC×GC) with accurate mass time-of-flight mass spectrometry (accTOFMS) to study oxidized species in complex thermally oxidized conventional and alternate aviation fuel matrixes. Tens of thousands of unique compounds were identified in the fuels, highlighting the need for comprehensive separations. GC×GC operation allowed a range of oxidized species to be isolated and identified, and in a conventional fuel, a series of homologous aldehydes and 2-ketones were found. 4-Methyl-2-hexanone and 1-pentanol were found to be strongly correlated with established methods for quantitatively assessing fuel stability.