This paper proposes a methodology for thermodynamic model analysis of Jatropha biodiesel engine in combination with Taguchi's optimization approach to determine the optimum engine design and operating parameters. A thermodynamic model based on two-zone Weibe's heat release function has been employed to simulate the Jatropha biodiesel engine performance. Among the important engine design and operating parameters 10 critical parameters were selected assuming interactions between the pair of parameters. Using linear graph theory and Taguchi method an L(16) orthogonal array has been utilized to determine the engine test trials layout. In order to maximize the performance of Jatropha biodiesel engine the signal to noise ratio (SNR) related to higher-the-better (HTB) quality characteristics has been used. The present methodology correctly predicted the compression ratio, Weibe's heat release constants and combustion zone duration as the critical parameters that affect the performance of the engine compared to other parameters. (C) 2009 Elsevier Ltd. All rights reserved.