Flaxseed is increasingly being used in some food products because of its high content of α‐linolenic acid and dietary fibre. However, flaxseed contains cyanogenic glycosides which release toxic hydrogen cyanide in the presence of water (autohydrolysis). A method for estimation of cyanide in flaxseed under these conditions is described. The determination is carried out by homogenizing the sample with water, letting it stand, filtering it through a membrane and then injecting the filtrate into an HPLC system consisting of an anion exchange column and an electrochemical (amperometric, oxidation) detector. The homogenate is analysed at various intervals until a maximum value of cyanide is observed. The cyanide content of ten cultivars of flaxseed, when analysed by this method, was found to range from 124 to 196μg/g. The release of cyanide showed a maximum at about 3h of hydrolysis. Virtually no cyanide was detected on boiling the homogenate or the flaxseed before determination.