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Biodiesel, an alkyl ester of plant oils that can be used in an unmodified diesel engine, is the first renewable diesel fuel alternative to become a commercially accepted part of our nation’s energy infrastructure. For traditional diesel fuel exhaust, it has been demonstrated that the particulate matter (PM) organic components play a role in acute inflammatory reactions. However, there have been only a few cytotoxicity and mutagenicity studies on biodiesel emissions. In this study, BEAS-2B cells, a transformed human airway epithelial cell line, were exposed in vitro to the PM organic extracts from Standard Reference Material (SRM) 1975, soy ethyl ester (SEE), soy methyl ester (SME), and petroleum diesel for 24 hours. This study demonstrated that the organic extracts of biodiesel PM in an aqueous solution can increase the release of pro-inflammatory cytokines IL-8 and IL-6 by respiratory epithelial cells. On a microgram PM equivalent per ml (µg PM eq/ml) basis, exposure to biodiesel extracts was associated with a greater release of IL-8 and IL-6 relative to organic extracts of two diesel PM samples. The dose range tested was not cytotoxic. It was also noted that the solvent exchange method, which was used to prepare the aqueous exposure doses, may not be appropriate for the investigation of biodiesel extracts, though it has been used extensively in petroleum diesel research. A valuable new finding from these experiments is that the soluble organic fraction (SOF) of biodiesel PM begins to elicit a cytokine response in BEAS-2B cells at an exposure lower than petroleum diesel PM extract (approximately 40 µg PM eq/ml). However, more research is required to better characterize the potency of the organic fraction of biodiesel compared to petroleum diesel.