BACKGROUND: Production of recombinant virus-like particles (VLPs) in yeast expression systems for use as vaccines requires cell disruption and detergent-mediated steps to liberate the product. Typically, these release high levels of cellular components such as lipids that foul chromatography columns. This study compares the impact of applying lipid-rich and lipid-depleted feedstocks to hydrophobic interaction chromatography columns to quantify the loss of performance caused by the presence of host lipids over a total of 40 operational cycles. RESULTS: VLP binding capacity in the lipid-rich feed was significantly lower than for the lipid-depleted feed, with greater than 24% of the lipids remaining in the column after each cycle. Triacylglycerol was found to be the major contaminant. The effectiveness of subsequent caustic clean-in-place was limited, resulting in column hydrophobicity increasing over repeated loading cycles. This improved the effective VLP binding capacity and affinity, but also made product elution more difficult, and recovery decreased by more than 70% over the 40 cycles. CONCLUSION: Host cell lipids cause major fouling problems during VLP purification. Instead of screening for better CIP conditions, priority should be given to identifying suitable upstream lipid removal strategies in order to maintain column performance and so yield more economically viable processes. (c) 2009 Society of Chemical Industry