Microfluidic cell culture devices have been used for drug development, chemical analysis, and environmental pollutant detection. Because of the decreased fluid volume and increased surface area to volume ratio, interactions between device surfaces and the fluid is a key element that affects the performance and detection accuracy of microfluidic devices, particularly if fluid is recirculated by a peristaltic pump. However, this issue has not been studied in detail in a microfluidic cell culture environment. In this study, chemical loss and contaminant leakage from various polymer surfaces in a microfluidic setup were characterized. The effects of hydrophilic coating with Poly (vinyl alcohol), Pluronic (R) F-68, and multi-layer ionic coating were measured. We observed significant surface-adsorption of estradiol, doxorubicin, and verapamil with PharMed (R) BPT tubing, whereas PTFE/BPT and stainless steell BPT hybrid tubing caused less chemical loss in proportion to the fraction of BPT tubing in the hybrid system. Contaminants leaching out of the BPT tubing were found to be estrogen receptor agonists as determined by estrogen-induced green fluorescence expression in an estrogen responsive Ishikawa cell line and also caused interference with an estradiol enzyme-linked immunosorbent assay (ELISA) assay, Stainless steel/BPT hybrid tubing caused the least interference with ELISA. In summary, polymer surface and chemical interactions inside microfluidic systems should not be neglected and require careful investigations when results from a microfluidic system are compared with results from a macroscale cell culture setup. (C) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 25: 543-551, 2009