Methyl esters of soybean oil, known as biodiesel, are 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 produces a higher fraction of soluble organic material (SOF) in the exhaust particulate matter than petroleum-based diesel fuel although its total particulate emissions were lowered. Also, because biodiesel has a high boiling point and low volatility compared with diesel fuel, its unburned hydrocarbon vapor could be lost by deposition in the hydrocarbon sampling line. This loss could be the source of reported reductions in hydrocarbon emissions from biodiesel-fueled engines. No information about whether the typical measurement temperature for unburned hydrocarbons is suitable for biodiesel hydrocarbon measurement is available. In this project, the formation of SOF in diesel exhaust particulates and the deposition of hydrocarbons in heated sampling lines were studied experimentally and theoretically;The experimental results showed 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 filter temperature at constant dilution ratio and with increasing dilution ratio at constant filter temperature. Biodiesel injection tests, where a small quantity of neat biodiesel was injected into the exhaust gas showed that most of the unburned biodiesel showed up in the soluble organic fraction of the collected particulates. The response of the heated flame ionization detector did not match the concentration change of unburned biodiesel in the exhaust gas. Based on the predicted results from condensation and multicomponent adsorption models, adsorption of vapor phase hydrocarbons on the carbon particle surface is the primary source of the SOF in the total particulate matter. The condensation process, by itself, cannot explain the formation of SOF during the dilution process. Adsorption of hydrocarbons is also shown to take place during transport of the hydrocarbon sample, even at high temperature. At the standard hydrocarbon measurement temperature, adsorption onto the sampling line walls could affect the concentration of unburned hydrocarbons and biodiesel in the exhaust gas sample. However, when the hydrocarbon sampling line temperature was heated to 250°C, adsorption did not show significant effect on reducing the hydrocarbon concentration in the exhaust sample.