This study is aimed at investigating the effect of injection system parameters such as injection pressure, injection timing and nozzle tip protrusion on the performance and emission characteristics of a twin cylinder water cooled naturally aspirated CIDI engine. Biodiesel, derived from pongamia seeds through transesterification process, blended with diesel was used as fuel in this work. The experiments were designed using a statistical tool known as Design of Experiments (DoE) based on response surface methodology (RSM). The resultant models of the response surface methodology were helpful to predict the response parameters such as Brake Specific Energy Consumption (BSEC), Brake Thermal Efficiency (BTE), Carbon monoxide (CO), Hydrocarbon (HC), smoke opacity and Nitrogen Oxides (NO(x)) and further to identify the significant interactions between the input factors on the responses. The results depicted that the BSEC, CO, HC and smoke opacity were lesser, and BTE and NO(x) were higher at 2.5 mm nozzle tip protrusion, 225 bar of injection pressure and at 30 degrees BTDC of injection timing. Optimization of injection system parameters was performed using the desirability approach of the response surface methodology for better performance and lower NO(x) emission. An injection pressure of 225 bar, injection timing of 21 degrees BTDC and 2.5 mm nozzle tip protrusion were found to be optimal values for the pongamia biodiesel blended diesel fuel operation in the test engine of 7.5 kW at 1500 rpm. (C) 2011 Elsevier Ltd. All rights reserved.