One of the main advantages of biodiesel fuels is that almost eliminate carbon dioxide emissions based on the CO2 consumption during plant growth. However it is accepted for most researchers that when burned in diesel engines there is an increase of the NOx emissions when these are compared to the NOx emissions produced by mineral diesel fuel. HCCI with diesel fuel is being considered as an alternative combustion process in the internal combustion engine, mainly because of the huge potential for simultaneous reduction of NOx and soot emissions while fuel conversion efficiency is not compromised, in fact, it is usually increased. The HCCI combustion process can accept a variety of fuel types, like biodiesel and mixtures with mineral diesel fuel. The main reason for burning biodiesel fuel in HCCI combustion mode is that it enables the simultaneous reduction of NOx and soot emissions to current standard requirements, as well as the elimination of CO2. This paper shows a methodology for HCCI combustion mode of biodiesel mixtures based on a high swirl ratio and EGR rate combined with late injection where HRR, NOx, CO, HC and soot emissions have been analyzed. This strategy has reduced fuel wall impingement encountered when early injection is used. Bowl in piston geometry has been designed with a dedicated swirling flow model and a NOx emission of biodiesel fuel has been reduced. (C) 2011 Elsevier B.V. All rights reserved.