The industry standard for measuring total exhaust hydrocarbons (HCs) in internal combustion engine exhaust is the flame ionization detector (FID); however, oxygenated HCs like those found in biodiesel or ethanol have reduced FID response and thus their true concentration is not accurately measured by conventional analyzers. This paper presents a new method to determine the response factor for the measurement of exhaust hydrocarbons using sample conditioning in combination with an analytical method. A custom designed variable temperature sample conditioner was designed and built and two fast FIDs were used determine the condensable fraction of hydrocarbons present in engine exhaust over a range of sample temperature. A correction model was developed to compensate for water condensing from the exhaust, nitrogen and carbon dioxide dissolving in the condensing water, and reduced response factor for HCs in the presence of water vapor. A theoretical model was developed to predict the condensation of unburned biodiesel as a function of temperature using a fatty acid profile of the fuel and Antoines equation for species vapor pressure. This model was used to estimate a relative response factor of 0.65 for unburned HCs in exhaust from a diesel engine operating on 100% biodiesel.