The use of biomass fuels for vehicles has been a focus of attention all over the world in terms of prevention of global warming, effective utilization of resources and local revitalization. For the purpose of beneficial use of unused biomass resources, the movement of the use of bioethanol and biodiesel made from them has spread in Japan.In Japan, biodiesel is mainly made from waste cooking oil collected by local communities or governments, and in terms of local production for local consumption, it is used as neat fuel (100% biofuel) or mixed with diesel fuel in high concentration for the vehicles. On the other hand, extremely low emission level must be kept for not only gasoline vehicles but also diesel vehicles in the post new long-term regulation implemented from 2009 in Japan. It is necessary for diesel vehicles to equip an advanced type of aftertreatment such as Urea-Selective Catalytic Reduction (SCR) system or lean NOx trap (LNT) catalyst system in order to comply with this regulation.In this study, engine bench tests were conducted to understand the emission characteristics in the use of high concentration of biodiesel for an engine system with the urea-SCR system which is expected to be equipped for a lot of heavy-duty vehicles in the near future.The results indicated that NOx emission in biodiesel operation increased compared with that in conventional diesel operation under Japanese JE05 mode test. This is because of the NOx emission increasing in the engine out and the NOx reduction efficiency decreasing in the urea-SCR system. Especially, B100 (Neat biodiesel) increased NOx emission over the New Long-Term regulation limit, even though this engine system complied with the new long-term regulation level enough. This was mainly affected by the decrease of NOx reduction efficiency in urea-SCR system due to the decrease of NO₂/NOx ratio at the inlet of urea-SCR.The factor of the decrease in NO₂/NOx ratio was considered to be the decrease in NO₂ concentration derived from the reduction of engine-out NO₂ emission and the deterioration of oxidizability of diesel oxide catalyst (DOC). As for the deterioration of oxidizability of DOC, it was thought to be due to the decrease in exhaust gas temperature, catalyst poisoning and reduction action by SOF adhered in DOC. Therefore, it was necessary to improve oxidizability of DOC in order to decrease NOx emissions.