This is the final report of the High Efficiency Clean Combustion (HECC) Research Program for the U.S. Department of Energy. Work under this co-funded program began in August 2005 and finished in July 2010. The objective of this program was to develop and demonstrate a low emission, high thermal efficiency engine system that met 2010 EPA heavy-duty on-highway truck emissions requirements (0.2g/bhp-hr NOx, 0.14g/bhp-hr HC and 0.01g/bhp-hr PM) with a thermal efficiency of 46%. To achieve this goal, development of diesel homogenous charge compression ignition (HCCI) combustion was the chosen approach. This report summarizes the development of diesel HCCI combustion and associated enabling technologies that occurred during the HECC program between August 2005 and July 2010. This program showed that although diesel HCCI with conventional US diesel fuel was not a feasible means to achieve the program objectives, the HCCI load range could be increased with a higher volatility, lower cetane number fuel, such as gasoline, if the combustion rate could be moderated to avoid excessive cylinder pressure rise rates. Given the potential efficiency and emissions benefits, continued research of combustion with low cetane number fuels and the effects of fuel distillation are recommended. The operation of diesel HCCI was only feasible at part-load due to a limited fuel injection window. A 4% fuel consumption benefit versus conventional, low-temperature combustion was realized over the achievable operating range. Several enabling technologies were developed under this program that also benefited non-HCCI combustion. The development of a 300MPa fuel injector enabled the development of extended lifted flame combustion. A design methodology for minimizing the heat transfer to jacket water, known as precision cooling, will benefit conventional combustion engines, as well as HCCI engines. An advanced combustion control system based on cylinder pressure measurements was developed. A Well-to-wheels analysis of the energy flows in a mobile vehicle system and a 2nd Law thermodynamic analysis of the engine system were also completed under this program.