For both the hydrolysis of vegetable oils and the esterification of glycerol and fatty acids hollow fibre membrane bioreactors are developed. In these bioreactors, hydrophilic membranes are used as immobilization carrier for the enzyme as well as phase separator. In this paper, the membrane reactor is scaled up from a 0.8 m(2) lab scale module to a 22.5 m(2) bench scale unit. In spite of cleaning, hardly any oil flow was possible through the fibre lumen within 3 months of operation. To study these phenomena, a series of lab scale experiments hydrolyzing sunflower oil was performed. During 40 days the cross-sectional area of the fibres decreased to 20% of its initial value. As a result, the hydrolysis activity of the bioreactor decline for 94%. Two possible fibre blocking mechanisms could be eliminated: enzyme coagulation and substrate/product polymerization. We found that fibre blocking was caused by swelling of the polyurethane potting. Swelling led to a decrease of the available volume for the membrane fibres embedded in the polyurethane potting, hence the how resistance in the lumen increased. Potting material immersed in short chain fatty acids gave a more rapid swelling than immersed in longer chain fatty acids. Similar to this, in a reactor running with a short tail fatty acid, oil flow was not possible any more after 5 days, while the use of oleic acid gave no fibre blocking, on the same time scale. In many types of hollow fibre membrane modules, polyurethane is used as potting resin. The use of these modules in membrane bioreactors or in any other two-phase membrane system could lead to flow problems.