Protein fractionation by ultrafiltration has elicited considerable interest in recent years. It is now recognised that a proper choice of the membrane and/or appropriate adjustment of operating conditions can successfully resolve binary protein mixtures. However, in order to identify the optimum conditions for selective filtration, it is essential to understand the UF characteristics of single proteins. In this paper, we have examined the flux and transmission behavior of three different proteins, viz. lysozyme (13.93 kD, pI 10.6), ovalbumin (43.5 kD, pI 4.6) and myoglobin (16.89 kD, pI 6.8) as a function of operating variables in a vortex flow filter using 100 kD hydrophilic polyacrylonitrile membranes. The effects of both the module hydrodynamics, i.e. transmembrane pressure, axial velocity and rotation speed as well as the solution environment, i.e. protein concentration, ionic strength and pH were investigated. It was determined that hydrodynamics is primarily controlled by the transmembrane pressure and the membrane rotation rate. Also, variations in the feed solution properties, particularly the ionic strength and pH could dramatically alter the protein transmission profiles. These results provide a basic framework for designing effective lysozyme/ovalbumin and lysozyme/myoglobin separations.