International Energy Agency envisages that advanced biofuels will contribute significantly to reducing emissions by increasing from 2-3% of total transport energy supply today to 27% by 2050. Transportation experts propose that R & D of next-generation biofuels must be carried out in conjunction with the development of advanced combustion engines.At present very intensive R & D works are being conducted by all major internal combustion (IC) engine manufacturers on the development of engine designs capable to work on blends with up to 100% of biofuel. Similar works are being conducted on retrofitting the old park of motors. The main challenge in such activities is to satisfy EU regulations on emission levels. To successfully achieve this goal it is necessary to carry out a combination of fundamental theoretical and experimental research. One of barriers in conducting theoretical part of investigations is absence of specialised software dedicated to accurate modelling the operation of IC engines on different biofuel blends and which would allow developers to optimise the working process strategy and design parameters of engines.The main objective of the “Bio-Green-IC-Engine” project is the creation of the extensive database on properties of biofuels, development of the advanced multizone thermodynamic model for the simulation of IC engines operating on various advanced biofuels and incorporating it into user-friendly software for rapid optimization of high performance clean engine design parameters. The accuracy of the deployed model will be enhanced by using data from three-dimensional CFD modelling of the fuel spray evolution and detailed chemistry analysis of biofuels combustion.The developed software will be used for industrial, research and educational purposes across EU countries and will improve the technological and industrial practice related to manufacturing IC engines and their fuel supply systems to operate on advanced biofuels.