The methyl ester of soybean oil, known as biodiesel, is receiving increasing attention as an alternative fuel for diesel engines. Biodiesel is a nontoxic, biodegradable, and renewable fuel with the potential to reduce engine exhaust emissions. However, previous results have shown that biodiesel-fueled engines produce a higher fraction of soluble organic material (SOF) in their exhaust particulate matter than when petroleum-based diesel fuel is used even when the total particulate emissions are lowered. Most researchers have also observed that unburned hydrocarbon (HC) emissions decrease with biodiesel. In this project, the formation of SOF in exhaust particulates under different measurement conditions and the possibility of deposition of HC vapor in the sampling lines of the HFID detector were studied experimentally and theoretically when the diesel engine was fueled with biodiesel.The experimental results confirmed that biodiesel produced a higher SOF fraction in its total particulates than diesel fuel under virtually all engine operating conditions. The SOF fraction decreased with increasing particulate filter temperature at constant dilution ratio and with increasing dilution ratio at constant filter temperature. The modeling results show that adsorption of vapor phase biodiesel on the carbon particle surface is the primary source of the SOF in the total particulate matter. The loss of vapor phase biodiesel due to adsorption is also shown to take place during transport of the engine exhaust sample in the heated sampling line, even at high temperature.