Abstract: A method is provided for controlling production of low molecular weight heparin (LMW-heparin) when depolymerizing heparin with heparinase in a reaction mixture in a reactor. Depolymerization to a desired average molecular weight is monitored by measuring an increase in UV-absorption (preferably at 230-235). When the absorption has reached a value for a desired molecular weight, the depolymerization is stopped or LMW-heparin having the desired molecular weight is continuously removed from the reaction mixture. In a preferred embodiment, the reaction mixture is subjected to ultrafiltration to produce a filtrate containing LMW-heparin, and a retentate which is recycled to the reactor. UV-absorption and refractive index of the filtrate are measured, and depolymerization is controlled in accordance with the measured absorption and refractive index to produce a filtrate containing a LMW-heparin of low polydispersity and predetermined molecular weight.