Protein fouling remains a major problem in the use of microfiltration for many bioprocessing applications. Experiments were performed to evaluate the effect of membrane morphology and pore structure on protein fouling using different track-etched, isotropic, and asymmetric microfiltration membranes. Fouling of membranes with straight-through pores occurred by pore blockage caused by deposition of large protein aggregates on the membrane surface. However, the rate of blockage was a function of the membrane porosity due to the possibility of multiple pore blockage by a single protein aggregate on high porosity membranes. Membranes with interconnected pores fouled more slowly since the fluid could flow around the blocked pores through the interconnected pore structure. This behavior was quantified using model membrane systems with well-defined pore morphology constructed from track-etch and isotropic membranes in a layered series combination. These results provide important insights into the effects of membrane pore structure and morphology on protein fouling.