Heparin is an anticoagulant used in extracorporeal procedures such as hemodialysis and open heart surgery. Unfortunately: heparin may induce potentially fatal complications in patients at high risk of bleeding. The use of art immobilized heparinase I reactor makes heparin therapy safer; but the design of a safe and efficient reactor for medical use had been a significant problem. A novel reactor, based on simultaneous separation-reaction and Taylor-Couette flow, was designed and successfully tested in vitro with human blood and ex vivo in sleep. The objective of this study was to understand the flow dynamics in the reactor in order to predict and optimize heparin neutralization. Residence-time distribution studies were performed and a mathematical model was developed The model was able to predict experimental conversions within a mean relative error of 5.5%. Bypass flow through the reactive section was also predicted.