The trace polar species present in diesel were investigated by combining selective ionization with high-resolution mass spectrometry. To eliminate matrix effects, the polar fraction was extracted using methanol and direct infusion with electrospray ionization and mass analysis were performed. The advantages and limitations of time-of-flight mass spectrometry and Fourier transform ion cyclotron resonance mass spectrometry for diesel analysis were discussed. Complementary information was obtained by considering both positive- and negative-ion mass spectra in terms of compounds that form part of the inherent fuel composition and compounds that represent fuel additives. In addition, diluted fuels were separated by gas chromatography prior to atmospheric pressure chemical ionization and mass analysis. Results showed that a large portion of unsaturated polycyclic hydrocarbons were not detected during direct infusion experiments, indicating that these species were not extracted efficiently with methanol and/or ionized efficiently with electrospray.