A capillary electrophoresis method with reversed polarity, combining both the application of a voltage and a pressure gradient between the buffer vials, was developed for the analysis of eight heparin-derived Δ-disaccharides obtained by enzymatic depolymerization. A 60 mM formic acid buffer at pH 3.40 was selected as running electrolyte, with an applied voltage of -15 kV and an overimposed pressure gradient (3.45.10 - 3 MPa) for 6 min from inlet to outlet starting at 20 min. Figures of merit such as run-to-run and day-to-day precision, and limits of detection were established. The electrophoretic method was applied to the analysis of depolymerization products of different kinds of heparins. The composition of the depolymerization buffer was selected in order to reduce baseline distortions in the electrophoretic separation, thus a buffer solution containing 20 mM Tris, 50 mM sodium chloride, and 3 mM calcium chloride at pH 7.10 was used. Percentages of molar disaccharide compositions for unfractionated heparins from porcine, bovine and ovine intestinal mucosa, and bovine lung were determined. In addition, low-molecular-mass heparins from bovine and porcine intestinal mucosa were analysed as well.