Cyanogen bromide activated agarose is widely employed as the water‐insoluble matrix in immunoadsorption and affinity chromatography for the immobilisation of proteins. A reaction mechanism is presented for the cyanogen bromide activation of the galactan, agarose, the coupling of model amines to the activated carbohydrate matrix and the detachment of ligands. Dansyl (Dns) derivatisation of the acid hydrolysed and unhydrolysed amine derivatives resulting from the reaction of cyanogen bromide‐activated Sepharose® and N‐α‐acetyl‐L‐ornithine reveal the production of arginine, indicating that the amine‐Sepharose conjugate is an O‐substituted isourea. Thin layer chromatography of the Dns‐derivatised unhydrolysed filtrate from the reaction indicated the formation of several derivatives which suggest that the isourea bonds can be cleaved by the solvolytic attack of nucleophiles in the pH range 8–9.5. Nucleophilic attack by amino groups on the amine‐Sepharose conjugates releases N‐monosubstituted guanidine, N1, N2 disubstituted ornithine and substituted ureas.