Ultrafiltration is used extensively for the purification of therapeutic biomolecules, with the behavior of proteins well-described using available hard-sphere models. The objective of this study was to examine the role of molecular flexibility in the ultrafiltration of plasmid DNA and PEGylated proteins, two important classes of next generation therapeutics. Plasmid DNA transmission was strongly dependent on the filtrate flux with very high transmission (>60%) obtained at the highest flux even though the radius of gyration of the plasmid was an order of magnitude larger than the membrane pore size. This behavior was consistent with models for infinitely flexible polymers accounting for elongation/deformation in the flow-field above the pore, although the elongation became significant at very small Deborah numbers using the available theory. In contrast, the transmission of PEGylated proteins was controlled by hard-sphere interactions at low filtrate flux, with the covalently attached polyethylene glycol (PEG) chains increasing the effective size of the biomolecule. However, there was clear evidence of elongation at high flux, particularly for PEGylated proteins linked to larger molecular weight polyethylene glycol chains. These results provide important insights into the role of biopolymer flexibility on the ultrafiltration characteristics of these second-generation biotherapeutics.