Hydroperoxides are major products of the autoxidation of hydrocarbon fuels and play a central role in oxidation kinetics. The quantification of hydroperoxide is a key factor for the qualification of jet-fuel and is determined through a standardized method. A recent comparison of different iodometric methods of quantification showed that an HPLC chain coupled with a post-reaction column (HPLC-PcR) is highly accurate with a high reproductivity 1. In this work, HPLC-PcR is used to detect and quantify the hydroperoxide content and analyze different oxidized surrogate fuels, by separating the oxygenated fractions. Surrogate fuels were oxidized in a PetroOxy and in a microreactor and then analyzed by HPLC-PcR. n-decane and cumene were used as surrogate jet-fuels and n-butanol as a surrogate biofuel. The oxidation of n-decane yields several decane hydroperoxides and other oxygenated compounds that were separated in the HPLC. The separated fractions of aged cumene in HPLC-PcR were analyzed by Gas Chromatography -Mass Spectrometry (GC-MS) and we demonstrate that the typical hydrocarbon oxidation pathways take place for cumene autoxidation, yielding only cumene hydroperoxide, 2-phenyl-2-propanol and acetophenone. On the contrary, for n-butanol, we demonstrate that the typical mechanism leading to ROOH does not prevail and that its autoxidation mainly yields H2O2 as peroxide content.