Homogeneous charge compression ignition (HCCI) is a combustion technology which has received increased attention of researchers in the combustion field for its potential in achieving low oxides of nitrogen (NOx) and soot emission in internal combustion (IC) engines. HCCI engines have advantages of higher thermal efficiency and reduced emissions in comparison to conventional internal combustion engines. In HCCI engines, ignition is controlled by the chemical kinetics, which leads to significant variation in ignition time with changes in the operating conditions. This variation limits the practical range of operation of the engine. Additionally, since HCCI engine operation combines the operating principles of both spark ignition (SI) and compression ignition (CI) engines, HCCI engine parameters such as compression ratio and injection timing may vary significantly depending on operating conditions, including the type of fuel used. As such, considerable research efforts have been focused on establishing optimal conditions for HCCI operation with both conventional and alternative fuels. In this study, numerical simulation is used to investigate the effect of compression ratio on combustion and emission characteristics of an HCCI engine fueled by pure biodiesel. Using a zero-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 in Chemkin-Pro. Simulation results are validated with available experimental data in terms of incylinder pressure and heat release rate to demonstrate the accuracy of the simulation model in predicting the performance of the actual engine. Analysis shows that an increase in compression ratio leads to advanced and higher peak incylinder pressure. The results also reveal that an increase in compression ratio produces advanced ignition and increased heat release rates for biodiesel combustion. Emission of NOx is observed to increase with increase in compression ratio while the effect of compression ratio on emissions of CO, CO2 and unburned hydrocarbon (UHC) is only marginal.