Sequential multidimensional gas chromatographic separations were used to identify secondary and tertiary oxidation products in a number of conventional fossil and alternatively derived aviation fuels. The samples were produced by low-temperature thermal oxidation of the fuels, and the higher dimensional separations were required because of the difficulty in quantification of the products at both bulk and molecular levels. The presence of certain oxidation products is a concern because of functional similarities to restricted contaminants, contribution to solid deposit formation, and impact on physical properties. Accurate identification assisted in characterization of a range of products. Primary alcohols dominated the secondary oxidation products in most cases, comprising 24-78% of the total oxygenated species identified in each fuel. Fuels were also subjected to several standardized physical property tests, showing that thermal oxidative stress affects certain fuel properties in a quantifiable manner, which, in some cases, is comparable to the effect of adding polar dopants.