This invention refers to the process for preparing low molecular weight heparins (LMWH) and very low molecular weight heparins (VLMWH) that comprises the steps of transalification of heparin into benzalkonium heparinate; depolymerisation in organic medium and transalification to form a salt of an alkali or alkaline earth metal. This invention also refers to the product obtained through the process described in this invention.