Effects of biodiesel fuel on nucleation mode particles were studied on a direct injection, high pressure common-rail diesel engine for passenger cars. Particle number and size distribution of the diesel engine were obtained using an Engine Exhaust Particle Sizer (EEPS). The base petroleum diesel, three different blend ratios of petroleum diesel/biodiesel (10%, 20% and 50% v/v biodiesel blend ratios), and the pure biodiesel fuel (obtained and converted from Jatropha seed in China) (B0, B10, B20, B50 and B100 fuels) were tested without engine modification. Experiments were performed on a series of engine operating conditions. The particle number size distribution of the engine shows unimodal or bimodal log-normal distribution. With the biodiesel blend ratios increasing, the number of nucleation mode particles increases at all test engine operating conditions and accumulation mode particles decreases at most engine operating conditions. Three mechanisms could lead to more nucleation mode particles formation: First, biodiesel fuel reduce soot emission and the solid soot surface lessen, and the ability of SOF condensation and adsorption on the soot particles weakens, so high super-saturation may lead to form new particles by nucleation. Second, increased viscosity and lower volatility of biodiesel fuel could lead that evaporation and air mixing in local area of combustion chamber was slower and bad comparing with pure diesel fuel, this may cause SOF increasing, and may lead to nucleation mode particles increasing because these particles mainly consist of SOF. Third, oxygen content of biodiesel fuel causes carbonaceous particle changing from fine size to ultrafine size or nano-particle size, also results in increase of nucleation mode particles.