Fuel-air mixing and combustion in engines are complex phenomena involving several subprocesses, wherein the availability (exergy) of the working fluid could be destroyed owing to irreversibilities or could be lost during energy exchanges. In the present work, a quasi-dimensional multi-zone engine model is used to quantify the availability destructions and losses associated with various mixing and combustion subprocesses in a heterogeneous charge compression ignition engine. This second-law analysis helps us to estimate the contributions of individual subprocesses towards the overall availability deficit. The results indicate that most of the availability destruction prior to ignition occurs because of fuel vaporization and mixing, whereas chemical reaction accounts for up to half of the total availability deficit during combustion. In-cylinder pressure equilibration and mixing of the combustion products with spray gases have major roles in availability destruction during the premixed combustion phase and the mixing-controlled combustion phase respectively. The contributions of wall heat transfer, heat transfer from the spray to the surrounding air and mixing of entrained air with spray gases assume significance in the later stages of combustion. Parametric studies indicate that reducing the in-cylinder air swirl and retarding the injection timing effectively curtail the availability deficit, thus improving the exergetic efficiency. © The Author(s) 2011.