Understanding the effects of membrane fouling on system capacity is critical for the successful design and scale-up of microfiltration systems. The underlying morphology and structure of the microfiltration membrane can have a significant effect on system capacity by altering the rate and extent of fouling. Experimental data were obtained for system capacity during protein microfiltration using several model membranes with both homogeneous and composite structures. Data were compared with predictions of a new model that can account for both pore blockage and cake formation, and also includes the effects of membrane morphology on internal flow profiles within the membrane. Membranes with highly interconnected pores have a significantly higher capacity due to the reduction in flux decline arising from the fluid flow under and around any surface blockage. The model calculations are in good agreement with the flux decline data, allowing far more accurate predictions of system capacity than for the commonly used V-max analysis. (C) 2003 Wiley Periodicals, Inc.