Carbon monoxide (CO) is a gaseous pollutant with adverse effects on human health and the environment. Industrial chemical processes contribute significantly to CO accumulation in the atmosphere. One of the most important processes for controlling carbon monoxide emissions is the conversion of CO to methanol by catalytic hydrogenation. In this study, the effects of two different flow types on the rate of CO removal along a two-stage hydrogen permselective membrane reactor have been investigated. In the first configuration, fresh synthesis gas flows in the tube side of the membrane reactor co-currently with reacting material in the shell side, so that more hydrogen is provided in the first sections of the reactor. In the second configuration, fresh synthesis gas flows in the tube side of the membrane reactor counter-currently with reacting material in the shell side, so that more hydrogen is provided in the last sections of the reactor. For this membrane system, a one-dimensional dynamic plug flow model in the presence of catalyst deactivation was developed. Comparison between co-current and counter-current configurations shows that the reactor operates with higher conversion of CO and hydrogen permeation rate in the counter-current mode whereas; longer catalyst life is achieved in the co-current configuration. Enhancement of CO removal in the counter-current mode versus the co-current configuration results in an ultimate reduction in CO emissions into the atmosphere. (C) 2010 Elsevier Ltd. All rights reserved.