Performance and particulate emissions of a modern common-rail and turbocharged diesel engine fueled with diesel and biodiesel fuels were comparatively studied. An electrical low-pressure impactor (ELPI) was employed to measure particle size distribution and number concentration. Two biodiesel fuels, BDFs (biodiesel from soybean oil) and BDFc (biodiesel from used cooking oil), as well as ultra-low sulfur diesel were used. The study shows that biodiesels give higher thermal efficiency than diesel. Biodiesels give obviously lower exhaust gas temperature than diesel under high engine speed. The differences in fuel consumption, thermal efficiency and exhaust gas temperature between BDFs and BDFc are negligible. The first peaks of heat release rate for biodiesels are lower than that of diesel, while the second peaks are higher and advanced for biodiesels. BDFs show slightly slower heat release than BDFc during the first heat release stage at low engine speed. BDFs and BDFc show similar heat release rate in the first heat release stage at high engine speed. HC and CO emissions maintain low values and vary little among three fuels. Biodiesels show lower CO2 emission. Biodiesels show lower NOx concentrations than diesel under low engine load; while at high engine load, biodiesels show higher NOx concentrations. BDFs gives higher NOx concentration than BDFc. Particle size distributions and geometric mean diameters for diesel and biodiesels are at the same level, while the total particle number concentration decreases by using biodiesels. BDFc shows lower number concentrations than BDFs at low engine speed, while the difference of number concentration between BDFs and BDFc is small at high engine speed. The study reveals that the particle number concentrations and mass concentrations can be reduced simultaneously when operating on biodiesels in the turbocharged common-rail injection diesel engine.