The often-observed differences in nitrogen oxides, or NOx, emissions between biodiesel and petroleum diesel fuels in diesel engines remain intense topics of research. In several instances, biodiesel-fuelled engines have higher NOx emissions than petroleum-fuelled engines; a situation often referred to as the "biodiesel NOx penalty." The literature is rich with investigations that reveal many fundamental mechanisms which contribute to (in varying and often inverse ways) the manifestation of differences in NOx emissions; these mechanisms include, for example, differences in ignition delay, changes to in-cylinder radiation heat transfer, and unequal heating values between the fuels.In addition to fundamental mechanisms, however, are the effects of "system-response" issues. With the application of biodiesel on an advanced technology diesel engine, the alteration to injection pulsewidth to match engine torque can make the engine controller change other control parameters of the engine, including: injection timing, rail pressure, exhaust gas recirculation (EGR) level, and variable geometry turbocharger (VGT) vane position. While it is clear the change in a control parameter (e.g., EGR) can have dramatic effect on NOx emissions, the analysis becomes complicated when considering the other system responses that could correspondingly occur (e.g., increased pressure difference between exhaust and intake manifold for flowing EGR). Thus, it becomes necessary to capture an understanding of the behavior and implications of such system responses.The objectives of this research study are to characterize NO and smoke concentrations in biodiesel compared to reference (i.e., petroleum) diesel, and to characterize the contributions of controlled system responses to the NO and smoke concentrations. These objectives are met by experimentally comparing 100% biodiesel (palm-olein) with 100% petroleum diesel and evaluating the engine's control parameters (e.g., EGR valve position, VGT position, turbocharger speed, and fuel rail pressure) and several measured parameters (e.g., NO and smoke concentrations, EGR level, exhaust and intake manifold pressures, and exhaust manifold temperature).This study identifies that controlled and passive changes to EGR can have similar effects on NO concentrations as does the often observed change to injection timing. For example, at conditions where biodiesel uses less EGR than petroleum diesel, NO concentrations increase by 15%. Correspondingly, the relative change in NO concentrations where EGR levels are consistent between the two fuels is insignificant. Consistent with observations reported in literature, biodiesel smoke concentrations are consistently lower; an average reduction of 78%.