Homogeneous charge compression ignition (HCCI) is one of the strategies for achieving low oxides of nitrogen (NOx) and soot emission in internal combustion engines. The HCCI engine has advantages of higher thermal efficiency and reduced emissions in comparison to conventional internal combustion engines. One of the special characteristics of an HCCI engine is that the ignition is controlled by the chemical kinetics, unlike the diesel or spark ignition engines for which ignition time can be controlled externally by the fuel injection or spark timing. The HCCI ignition time can therefore vary significantly with changes in the operating conditions, and this variation can limit the practical range of operation of the engine. In this study numerical simulation is used to investigate the effect of compression ratio on combustion and emission characteristics of an HCCI engine fuelled by pure biodiesel. Using Chemkin-Pro commercial simulation software’s 0-Dimensional (0-D) reactor model and a detailed reaction mechanism for biodiesel, the influence of compression ratio on the combustion and emission characteristics are studied. Simulation results are compared with published experimental data in terms of in-cylinder pressure and heat release rate to demonstrate the accuracy of the simulation model in predicting the performance of the actual engine. Analysis shows that by using the HCCI engine, a comparable power output can be obtained from pure biodiesel as compared to fossil diesel. The results also reveal that an increase in compression ratio produces advanced ignition and increased heat release rates for both diesel and biodiesel combustion. Emission of NOx is also observed to increase with increase in compression ratio. Compression ratio is however found to have no significant effect on emissions of CO, CO2 and unburned hydrocarbon (UHC).