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Biodiesel made from the transesterification of plant- and animal-derived oils is an important alternative fuel source for diesel engines. Although numerous studies have reported health effects associated with petroleum diesel emissions, information on biodiesel emissions are more limited. To this end, a program at the U.S. EPA assessed health effects of biodiesel emissions in rodent inhalation models. Commercially obtained soybean biodiesel (B100) and a 20% blend with petroleum diesel (B20) were compared to pure petroleum diesel (B0). Rats and mice were exposed independently for 4h/day, 5days/week for up to 6weeks. Exposures were controlled by dilution air to obtain low (50 mu g/m(3)), medium (150 mu g/m(3)) and high (500 mu g/m(3)) diesel particulate mass (PM) concentrations, and compared to filtered air. This article provides details on facilities, fuels, operating conditions, emission factors and physico-chemical characteristics of the emissions used for inhalation exposures and in vitro studies. Initial engine exhaust PM concentrations for the B100 fuel (19.7 +/- 0.7mg/m(3)) were 30% lower than those of the B0 fuel (28.0 +/- 1.5mg/m(3)). When emissions were diluted with air to control equivalent PM mass concentrations, B0 exposures had higher CO and slightly lower NO concentrations than B100. Organic/elemental carbon ratios and oxygenated methyl esters and organic acids were higher for the B100 than B0. Both the B0 and B100 fuels produced unimodal-accumulation mode particle-size distributions, with B0 producing lower concentrations of slightly larger particles. Subsequent papers in this series will describe the effects of these atmospheres on cardiopulmonary responses and in vitro genotoxicity studies.