The invention relates to a process for the depolymerization of glycosaminoglycanes characterized by the use of electron beam radiation, optionally in the presence of an organic compound selected from the group consisting of ethers, alcohols, aldehydes, amides and formic acid. The invention also relates to the intermediate depolymerized heparin obtained by the process. The intermediate depolymerized heparin can be dissolved in a buffer solution and fractionated by Gel Permeation for obtaining the desired Molecular Weight.