In this paper we describe the atomization and combustion characteristics of biodiesel fuels in a common-rail diesel engine. To investigate the effect of the mixing ratio of biodiesels on the emission characteristics and engine performance, the experiments were conducted at various mixing ratios of the biodiesel and engine operation conditions. In addition, the physical properties such as kinematic viscosity and cetane number of the biodiesel-blended fuel were analyzed to study relations with the fuel atomization and combustion characteristics. The atomization characteristics of biodiesel-blended fuels were investigated in terms of spray tip penetration, SMD, and mean velocity distributions by using a spray visualization system and phase Doppler particle analyzer. The effect of the mixing ratio on the combustion characteristics was studied on the basis of the results of the combustion pressure obtained from the single-cylinder engine at various experimental conditions. The emission characteristics of HC, NOx, and CO were also measured to reveal the effect of the mixing ratio of the biodiesel fuel on the pollutant emissions. The results indicate that the mean size of the droplets increases in accordance with the mixing ratio of the biodiesel because the viscosity and surface tension of the biodiesel are higher than those of the conventional diesel fuel. As the ratio of the biodiesel becomes higher, HC and CO emissions are decreased, whereas the NOx, emission increases because of oxygen in the biodiesel and a shorter ignition delay.