IC engines are facing two major challenges in the 21st century namely threat of fossil fuel depletion and environmental concerns. HCCI engine is an attractive solution to meet stringent emission challenges due to its capability to simultaneously reduce NOx and PM. HCCI technology can be employed with different alternative fuels without significant modifications in the existing engines. In this study, HCCI combustion was investigated using B20 (20% v/v biodiesel with diesel). Investigations were carried out on a two cylinder engine, in which one cylinder was modified to operate in HCCI mode however the other cylinder operated in conventional CI combustion mode. A dedicated fuel vaporizer was used for homogeneous fuel-air mixture preparation. The experiments were performed at three different intake charge temperatures (160°C, 180°C and 200°C) and three different EGR ratios (0%, 10% and 20% EGR) at different engine loads. In-cylinder pressure and exhaust emissions were measured under all test conditions, when the engine was stabilized. Physical characterization of engine exhaust particles was done for all these test fuels using engine exhaust particle sizer (EEPS). At higher engine loads, biodiesel HCCI showed slightly higher knocking tendency. With increasing EGR, knocking tendency reduced however in-cylinder pressure and heat release rate also reduced. Combustion characteristics of biodiesel HCCI improved with increasing intake charge temperature however high intake charge temperature caused excessive knocking and adversely affected performance characteristics. Biodiesel HCCI showed superior performance characteristics with increasing EGR due to optimization of combustion phasing. Due to excessive knocking, high intake charge temperature slightly reduced performance characteristics of mineral diesel. NOx emissions were very low for however HC and CO emission increased with increasing EGR. Increasing intake charge temperature reduced HC and CO emissions and increased NOx emissions at very high engine load. Particle emission characteristics showed that B20 combustion emitted slightly higher nano-particles which increased with increasing EGR and reduced with increasing intake charge temperature.