The analysis of fuels is not straightforward, due to its complex nature, and many different techniques have been developed to address this complexity. This paper reports on the use of hydrophilic interaction liquid chromatography (HILIC) as a complementary and green method for classifying diesel fuel composition. For comparative reasons, analyses with and without chromatographic preseparation were performed. Selective ionization of polar species was achieved with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI). High resolution time-of-flight mass spectrometry (TOFMS) was used to summarize the fuel composition in terms of compound classes based on accurate mass based elemental compositions. These compound classes showed different retention characteristics and were separated to a certain extent under hydrophilic interaction conditions. In normal phase liquid chromatography, the separation is based on heteroatom content, whereas alkylation (chain length) and degree of unsaturation (or double bond equivalents, DBE) play an important role in reversed phase liquid chromatography. The separation achieved with the proposed HILIC method depended on heteroatom content, DBE as well as hydrogen bonding, while alkylation did not influence retention significantly. This work therefore presents an alternative and complementary method for fuel analysis, compared to traditional reverse and normal phase liquid chromatography, by considering specific advantages and limitations.