This study is to investigate spray, combustion and emission characteristics of mixtures of diesel and soy-based biodiesel in a CI engine. A surrogate mechanism is developed by combining the skeletal mechanisms of methyl butanoate and n-heptane. Thermophysical properties are validated against measured tip penetrations and Sauter mean diameters (SMDs) of nonreacting sprays. Biodiesel shows spray characteristics of larger SMD's, lower volatility and slower mixing with ambient air due to larger viscosity and surface tension. Engine simulation is performed by the CMC-ISR model to resolve coupling between chemistry and turbulence. There is no noticeable difference in ignition delays of diesel and biodiesel, while flame propagates slower with slower evaporation and mixing for biodiesel. Results are in good agreement for pressure traces, NOx and trends of variation of CO and PM in a range of operating conditions. NOx decreased for BD < 60% and increased for BD > 60% with increasing biodiesel fraction, while PM and CO decreased due to the oxygen content in biodiesel in the test engine. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.