A compression ignition reciprocating internal combustion engine has been modified to allow operation with late direct injection of rapeseed biodiesel fuel blends. The purpose of these modifications is to reduce both the engine's carbon footprint and emission of nitrogen oxides and soot, without decreasing performance or using expensive emission post-treatment systems. The experimental part of this work is based on the measurement of the main pollutants being emitted and the analysis of the combustion process, which is accomplished by the study of the heat release rate curve. This curve is derived from the experimental chamber pressure data, in combination with a zero-dimensional thermodynamic model assuming a perfect mixing reactor with temporal variation in volume and chemical composition, temperature-dependent properties and heat losses. The analysis of the experimental results allows deepening the knowledge of the combustion process in a compression ignition engine with late direct injection using different biodiesel blends. There is a significant reduction (>50%) of emissions of nitrogen oxides in comparison with the original configuration. This allows considering the modified configuration as an advanced combustion mode, intermediate between conventional compression ignition engines and homogeneous charge compression ignition combustion mode.