Cleaning of membranes fouled with protein solutions is a common part of the normal operational procedure in membrane applications for the dairy and other food industries. Chemical cleaning with simple caustic and acid cleaners is still common practice although the response of different protein components in a foulant layer to cleaning agents is not well understood. This paper examines the efficiency of chemical cleaning of polyethersulfone (PES) membranes fouled during ultrafiltration of whey protein isolates solution and the protein residuals remaining on the membranes after cleaning. Using a combination of the Lowry assay and gel-electrophoresis for estimation of protein amount and composition on the membrane before and after cleaning, it was observed that the high molecular weight components in the foulant layer could more easily be removed than the smaller components, and the proteins trapped in the membrane pores were the most difficult to clean. In repeated cycles of filtration and cleaning with NaOH followed by HCl, the flux recovery due to NaOH cleaning remained constant after the 2nd cycle, while the flux recovery due to HCl cleaning increased with the repeated cycle, indicating the importance of HCl cleaning stage in the removal of residual protein components. (C) 2012 Elsevier B.V. All rights reserved.