Recent engine development has focused mainly on the improvement of engine efficiency and output emissions. The improvements in efficiency are being made by friction reduction, combustion improvement and thermodynamic cycle modification. New technologies such as Variable Valve Timing (VVT) or Variable Compression Ratio (VCR) are important for the latter. To assess the improvement capability of engine modifications, thermodynamic analysis of indicated cycles of the engines is made using the first and second laws of thermodynamics. The Entropy Generation Minimization (EGM) method proposes the identification of entropy generation sources and the reduction of the entropy generated by those sources as a method to improve the thermodynamic performance of heat engines and other devices. A computer model created and implemented in MATLAB Simulink was used to simulate the conventional Otto cycle and the various processes (combustion, free expansion during exhaust, heat transfer and fluid flow through valves and throttle) were evaluated in terms of the amount of the entropy generated. An Otto cycle, a Miller cycle (over-expanded cycle) and a Miller cycle with compression ratio adjustment are studied using the referred model in order to evaluate the amount of entropy generated in each cycle. All cycles are compared in terms of work produced per cycle.