Biorenewable fuels hold tremendous potential in the continuing efforts toward a sustainable future. Within the biorefinery paradigm membrane operations have the potential to reduce processing costs, reduce water demands, and provide opportunities for valuable co-product recovery. Here, ultrafiltration has been evaluated as a separation operation within a traditional corn ethanol process to recover high value native and/or recombinant proteins prior to the fermentation. Different membrane materials and molecular weight cut-offs have been investigated to determine optimal conditions for yield, selectivity, and throughput. In addition, different modeling approaches, along with spectroscopic and microscopic analyses were completed to identify fouling mechanisms and the most problematic fouling constituents within a complex corn kernel extract. It was found that inorganic ash compounds may have been the most likely species fouling regenerated cellulose membranes, while protein and other organic compounds may have been more problematic when using a polyethersulfone-based chemistry. A smaller pore size (5 kDa) reduced the fouling rate for both membrane materials compared to a larger pore size (100 kDa). The molecular weight cutoff did not have a significant effect on protein yield or purity. (C) 2010 Elsevier B.V. All rights reserved.