A simple, selective and accurate capillary electrophoresis (CE) method has been developed for the rapid separation and identification of various low molecular weight heparins (LMWHs) and unfractionated heparin. Separation and operational parameters were investigated using dalteparin sodium as the test LMWH. The developed method used a 70 cm fused silica capillary (50 m i.d.) with a detection window 8.5 cm from the distal end. Phosphate electrolyte (pH 3.5; 50 mM), an applied voltage of −30 kV, UV detection at 230 nm and sample injection at 20 mbar for 5 s were used. The method performance was assessed in terms of linearity, selectivity, intra- and inter-day precision and accuracy. The method was successfully applied to the European Pharmacopeia LMWH standard, dalteparin sodium, enoxaparin sodium and heparin sodium with a significant reduction in the run time and increased resolution compared with previously reported CE methods. Different CE separation profiles were obtained for various LMWHs and unfractionated heparin showing significant structural diversity. The current methodology was sensitive enough to reveal minor constituent differences between two different batches of enoxaparin sodium. This CE method also clearly showed chemical changes that occurred to LMWHs under different stress conditions. The sensitivity, selectivity and simplicity of the developed method allow its application in research or manufacturing for the identification, stability analysis, characterization and monitoring of batch-to-batch consistency of different low molecular weight and unfractionated heparins. © 2007 Elsevier B.V. All rights reserved.