The determination of the phenanthridine trypanocide, isometamidium chloride hydrochloride (ISM), in the presence of four process-related and degradation impurities, by RP-HPLC using a Licrospher-60 RP-select B column with a mobile phase composition of acetonitrile/KH2PO4 (PH 3.0, 20 mM) (25:75 v/v) with UV detection at 320 nm, is described. The method is selective, reproducible and precise with a limit of detection of 45 ng ml-1 for ISM. A HPTLC system (Kieselgel 60 F254, pyridine/acetonitrile/butanol/formic acid, 6:6:4:1, v/v), with UV densitometric evaluation at 320 nm, suitable for the separation of ISM and the related substances is reported.