In recent years, due to the limited resources and possible future shortage of fossil fuels, the production and utilization of alternative energy have been given increasing emphasis. Biodiesel fuels are considered to be very important renewable alternative fuels in the future. To study the combustion characteristics of biodiesel fuels, detailed kinetic mechanisms for several biodiesel surrogates have been recently developed [1, 2]. Fisher et al.  developed kinetic model for methyl butanoate which is the first mechanism used for engine simulation of biodiesel. Most recently, Togbe et al.  reported a kinetic mechanism for methyl octanoate, and Herbinet et al. reported detailed mechanisms for larger biodiesel surrogate methyl decanoate  and mono-unsaturated ester surrogate methyl decenoates . These detailed kinetic mechanisms enable the computational study of combustion simulation using biodiesel. In order to study the combustion behavior of biodiesel in engine simulations, it is important to use detailed chemistry within the computational fluid dynamics (CFD) model. However, integrating biodiesel surrogate mechanisms in CFD simulation is very computationally expensive due to the large number of species and reactions involved. There are a number of methods that exist in the literature for kinetic mechanism reduction, which are summarized in the review article by Lu et al. . In our previous work, an on-the-fly reduction approach  based on element flux analysis was developed and incorporated with CFD simulation . A multi-element flux analysis combining carbon and nitrogen element flux analysis was also employed to describe both the hydrocarbon chemistry and nitrogen chemistry in homogeneous charge compression ignition (HCCI) engine , through which the NOx emission characteristics can be captured. In the present study, the on-the-fly kinetic reduction approach is extended to incorporate large-scale biodiesel surrogate mechanisms with CFD simulation in HCCI engine. KIVA-3V [10 is used as the CFD framework for HCCI engine simulation. CHEMKIN [11 chemistry solver is incorporated in the KIVA-3V code to handle the chemistry calculation. The multi-element flux analysis is applied to study CO and NOx emission characteristics. Combustion characteristics and engine performance parameters, including ignition delay, total heat release, work done per cycle and power output, are calculated during the engine simulation. The slightly lower engine power and higher NOx emission for biodiesel predicted in this study is in agreement with some existing experimental and computational results [12, 13. Comparison between biodiesel and conventional diesel was conducted to evaluate the performance of biodiesel as an alternative diesel fuel.