Residual material from liquid-based cytology (LBC) samples, collected during cervical screening, is a valuable resource for molecular biological analysis. Because of the central role played by human papillomavirus (HPV) in the development of cervical cancer, assays are being developed to quantify HPV gene expression in LBC material. Using quantitative realtime PCR we have compared recovery of HPV DNA and RNA from two of the most widely used LBC systems (the ThinPrep system (Cytyc Corp.) and the SurePath system (TriPath Imaging, Inc.)). Recovery of RNA was unaffected by storage in ThinPrep media, however storage of cells in SurePath resulted in significantly reduced yields (between 10(4)- and 10(8)-fold reduction depending on extraction technique). Given the increasing prominence and importance of molecular diagnostics and prognostics this is an important finding, and must be considered in relation to choice of LBC system.