Sterile filtration is used to remove microorganisms in the processing of most recombinant proteins, but there are significant challenges in applying this technology to large biotherapeutics like Live-Attenuated Vaccines (LAV), lipid-nanoparticles, and gene therapy agents. Previous studies have reported highly variable fouling and product retention behavior of different sterile filters in these applications, but there has been no clear understanding of the origin of these differences. This study used fluorescently-labeled 200, 300, and 400 nm polystyrene latex spheres as model particle challenges for eight commercially available, 0.2/0.22 μm pore size sterile filters, all of which were characterized using mercury intrusion porosimetry, bubble point measurements, and scanning electron microscopy. All filters showed significant fouling, causing an increase in particle retention at high throughput. The maximum transmission of the 300 nm particles varied from only 0.01 for the highly asymmetric Millipore Express® to 0.9 for the dual-layer Sartobran® P. The transmission was well correlated with the ratio of the particle diameter to the maximum pore size (determined by bubble point), with even better agreement obtained using the mean pore size evaluated from mercury intrusion porosimetry. These results provide important insights into the effects of pore size and structure on the retention characteristics of sterile filter as well as guidance on how to select the best sterile filters for processing vaccines and viruses that are >100 nm in size.