This paper describes the results of on-board measurement of engine performance and emissions in diesel vehicle operated with bio-diesel fuels. Here, two waste-cooking oils were investigated. One fuel is a waste-cooking oil methyl esters. This fuel is actually applied to a garbage collection vehicle with DI diesel engine (B100) and the city bus (B20; 80% gas oil is mixed into B100 in volume) as an alternative fuel of gas oil in Kyoto City. Another one is a fuel with ozone treatment by removing impurities from raw waste-cooking oils. Here, in order to improve the fuel properties, kerosene is mixed 70% volume in this fuel. This mixed fuel (i-BDF) is applied into several tracks and buses in Wakayama City. Then, these 3 bio-diesel fuels were applied to the on-board experiments and the results were compared with gas oil operation case.Small size SUV with IDI diesel engine of 2.0 liter in engine displacement was utilized to conduct on-board experiments of vehicle performance and exhaust emissions. As an on-board measurement system, several sensors and devices were installed into the vehicle to detect vehicle position, ambient conditions, intake air conditions, fuel injection quantity, and exhaust emissions. Then, it is capable to measure the engine performance and emissions of PM as well as NOx in real time for actual traffic roads infrastructure including the town area, an intersection and an expressway.It is confirmed that road infrastructure, traffic conditions, driver's operation and so on affect engine performance and NOx, PM emissions. And, fuel consumption and NOx emission of bio-diesel fuels increases slightly comparing with gas oil case. On the contrary, PM emission of bio-diesel fuel is remarkably lower than that of gas oil at real traffic in the expressway. Here, it should be noticed that PM emission was measured by optical smoke meter in this study. However, there is little influence in fuel consumption and NOx, PM emissions for all fuels through the town area operation.