A selective removal of humic constituents involved in ester groups was conducted by a boron trifluoride-methanol transesterification reaction after removal of structurally unbound lipids. An analytical separation of subfractions containing specific classes of compound liberated from the humic matrix simplifies their identification by gas chromatography-mass spectrometry. We compared the traditional liquid-liquid separation into phenolic and aliphatic fractions with the modern and versatile fractionation technique using solid-phase extraction (SPE) on aminopropyl-bonded phases. Our results showed that both methods ensured separation of the same compounds, such as di- and tri-hydroxyalkanoic acids, alpha-, beta- and omega-hydroxy fatty acids, alkanoic acids, alpha,omega-alkanedioic acids, n-alkanols, phenolic acids and sterols. Moreover, the SPE method not only provided a larger recovery of compounds, but involved smaller sample and solvent requirements, and larger ease and rapidity of sample handling than the traditional liquid-liquid separation. The SPE method should be thus recommended in structural studies of natural organic matter.