This paper describes the optimization of compression ignition engines fueled with dimethyl ether (DME), an alternative to diesel fuel. In order to calculate in-cylinder flow and combustion processes, a KIVA code, coupled with the Chemkin chemistry solver, was used. The optimization processes were performed based on a micro-genetic algorithm with a population number of five for each generation. The optimization processes were performed for one hundred generations. In addition, the computational mesh generated an auto-mesh generator, which was able to produce a computational mesh based on the given parameters, such as cup depth and Beizer curve definitions. The optimized design for the DME engine was also compared to that of conventional diesel engines for combustion and emission characteristics. The results showed that significant merit value improvements were achieved for both DME and diesel engines with the presented optimization. For the optimized design of DME engines, the combustion and emission characteristics were significantly different from those of diesel engines because of differences in fuel properties. For conventional diesel engine cases, a 136% improvement in merit value was achieved during the optimization process from the baseline to the optimized design. (C) 2012 Elsevier Ltd. All rights reserved.