Humic acids (HAs) extracted from different organic compost and soil from Argentina have been characterized by capillary electrophoresis (CE) and mass spectrometry. The chemical properties of HAs show changes depending on their origin (compost, soil). Capillary electrophoresis analyses were carried out using a background electrolyte consisting of boric acid, TRIS and EDTA (BTE). BTE was also modified with cyclodextrins. After optimization of BTE, the best results were obtained when P-cyclodextrin was used. Under optimized separation conditions, the characteristics CE fingerprints of compost derived HAs (CHAs) were studied. CE fingerprints show differences in the composition of the different CHAs. Mass spectra obtained by laser desorption ionization time of flight mass spectrometry show differences between the CHAs and HAs extracted from Argentinean soil. A comparison with the soil standard HAs (International Humic Substances Society) was made. CHAs show mostly compounds in the mass spectra with low m/z values. The typical patterns exhibited in soil HAs of different origin are present in the Argentinean soil HA, i.e. groups of peaks around mass-to-charge (m/z) 800.