Main objective of this study is to compare performance and emission characteristics of a pilot injection diesel engine with the additions of alternative fuels like pure hydrogen, HHO and biodiesel. In order to achieve this goal, Helianthus annuus (sunflower) biodiesel was produced and blended with volumetric ratio of 10% with diesel fuel. Additionally, intake air was enriched with pure hydrogen or HHO via intake manifold without any structural changes except reduction of injected diesel fuel on the 3.6 L, four cylinders, four stroke diesel engines. Amount of Hydrogen fuel supplied to the engine was adjusted to constant 10 L/min during the experiments. The effects of pure hydrogen and HHO usage with the addition of biodiesel to the engine performance values (Brake Torque, Brake Power and Brake Specific Fuel Consumption) and exhaust emission values (NOx, CO2, CO) were investigated in between 1200 and 2600 rpm engine speeds. Engine performance values were increased with the enriching the intake air with HHO than pure hydrogen compared to the standard diesel fuel operating condition. On the other hand, in terms of exhaust gas emissions, pure hydrogen provided better results than HHO. In both cases, changes on the engine performance results were minimal however improvements on exhaust gas emissions were very promising. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.