Commercial pentosan polysulfate sodium salts (NaPPS) are highly sulfated polysaccharides derived from beechwood hemicellulose by sulfate esterification with a Mrel range of 1500—6000. The polysaccharide backbone of NaPPS consists of repeating linear units of 1—4 linked β‐D‐xylopyranose with laterally substituted 4‐methylglucopyranosyluronic acid units glycosidically linked to the 2 position of the main chain at every 10th xylopyranose unit on average. For many years NaPPS has been used for antithrombotic prophylaxis in Europe and interstitial cystitis in the USA and Australia. More recently NaPPS has found veterinary application for the treatment of osteoarthritis and related conditions in domestic animals and is registered for this use in Australia, New Zealand, Canada, UK, Eire, and several Scandanavian countries. At present the use of NaPPS for human disorders is confined to material manufactured by one company. However, for veterinary applications, NaPPS from three manufactures have been described. Since it is well known that the biological activities of sulfated polysaccharides are dependent on their molecular structures we considered it important to characterise these various NaPPS preparations using an established method of analysis. Unfortunately, traditional analytical techniques such as TLC, OR, UV/Vis spectroscopy, and size exclusion chromatography were incapable of providing structural information which would distinguish these NaPPS preparations from each other. In contrast, a capillary zone electrophoresis (CZE) method facilitated characterisation of the different NaPPS by a highly reproducible fingerprint, using a benzene‐1,2,4‐tricarboxylic acid buffer (8.75 mmol/L, pH = 4.9) with indirect UV detection (λ = 217 nm) and a special capillary pre‐treatment (1 M NaOH for 1 h at 25°C, then running buffer for 120 min at 25°C applying —20 kV). In the present study more than 20 batches of NaPPS from the three manufacturers have been investigated and compared. Minor batch variations were observed to exist for each manufacturer's product however significant differences were detected between NaPPS synthesised by the different manufacturers. Moreover, some preparations showed fingerprint profiles that indicated a more heterogeneous mixture, probably containing other polysaccharides as well.