The invention relates to a process for the depolymerization of glycosaminoglycanes characterized by the use of high-energy radiation 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 intermediate depolymerized heparin having a molecular weight of between 1,000 and 5,500, absorbance at 400 nm below 0.300 and ratio SO.sub.3.sup.-/COO.sup.-equal to or higher than in the starting heparin. The intermediate depolymerized heparin can be dissolved in a buffer solution and fractionated by gel permeation for obtaining the desired molecular weight.