The composition of diesel exhaust has changed over the past decade due to the increased use of alternative fuels, like biodiesel, and to new regulations on diesel engine emissions. Given the changing nature of diesel fuels and diesel exhaust emissions, a need exists to understand the human health implications of switching to "cleaner" diesel engines run with particulate filters and engines run on alternative fuels like biodiesel. We exposed well-differentiated normal human bronchial epithelial cells to fresh, complete exhaust from a diesel engine run (1) with and without a diesel particulate filter and (2) using either traditional petro- or alternative biodiesel. Despite the lowered emissions in filter-treated exhaust (a 91-96% reduction in mass), significant increases in transcripts associated with oxidative stress and polycyclic aromatic hydrocarbon response were observed in all exposure groups and were not significantly different between exposure groups. Our results suggest that biodiesel and filter-treated diesel exhaust elicits as great, or greater a cellular response as unfiltered, traditional petrodiesel exhaust in a representative model of the bronchial epithelium.