This PhD aspired to a develop greater insight into the fundamentals of hydrocarbon autoxidation processes in the context of thermal stability of aviation fuels. A number of approaches to develop a better understanding of the observed processes have been considered. This covers establishing the suitability of an automated reaction mechanism generator to develop autoxidation reaction mechanism as well as manipulating the resultant schemes, for example by lumping species and their associated reactions as well as reaction rate based mechanism reduction. Further a number of postulated interactions between contaminants in fuel and oxidised products in thermally stressed hydrocarbons employing ab initio quantum chemistry methods were examined. Finally a set of systematic experiments was carried out to obtain quantitative data of the effect of a number of additives on the stability of thermally stressed hydrocarbons. These tests employed a small scale test device, the PetroOxy which provides reliable and reproducible experimental data under well defined test conditions. The PetroOxy enabled the collection of samples of the deposition products on metal foils for further analysis under a scanning electron microscope with x-ray dispersive spectroscopy for elemental analysis. This provided both the morphology as well as the elemental distribution of the deposits formed on the foils, offering a first hand look at the differences between deposits formed from different additives. This thesis shows that automated mechanism generation is a suitable method when describing the initial steps of autoxidation processes without any additives. It further shows that the PetroOxy is a very useful tool for obtaining systematic, reliable, experimental data for further analysis.