Exhaust gas recirculation (EGR) has been employed in a diesel engine to reduce NOx emissions by diluting the fresh air charge with gases composed of primarily N2, CO2, H2O, and O2 from the engines exhaust stream. The addition of EGR reduces the production of NOx by lowering the peak cylinder gas temperature and reducing the concentration of O2 molecules, both of which contribute to the NOx formation mechanism. The amount of EGR has been typically controlled using an open loop control strategy where the flow of EGR was calibrated to the engine speed and load and controlled by the combination of an EGR valve and the ratio of the boost and exhaust back pressures. When oxygenated biofuels with lower specific energy are used, the engine control unit (ECU) will demand a higher fuel rate to maintain power output, which can alter the volumetric flow rate of EGR. In addition, oxygenated biofuels affect the oxygen concentration in the intake manifold gas stream. The following work utilized an analytical analysis of EGR and experimental engine data to compare a soy methyl ester biodiesel (B100) to ultra-low sulfur diesel fuel (B0) with respect to EGR rate, intake air dilution and oxygen concentration, fuel consumption, brake specific NOx and particulate matter emissions in a 1.9L turbocharged DI diesel engine. Analysis using the experimental data and analytical analysis compared an O2 based EGR measurement method to a CO2 based method and found the CO2 methods were more accurate than an O2 method when using a five-gas emissions analyzer. The analytical analysis indicated a 0% to 0.3% difference in the intake gas stream oxygen concentrations when a B100 test fuel was used but experimental measurements were inconclusive as the difference in oxygen concentration of the intake gas stream was within the accuracy limits of the emissions analyzer. Additional analysis revealed that the brake specific fuel consumption was higher and the particulate matter emissions were lower for the B100 test fuel at equivalent levels of power, EGR rate, and brake specific NOx emissions. Overall, changes to the fuel flow rate and EGR composition resulting from the use of the oxygenated biofuel had varying effects on the performance of the 1.9L diesel engine.