This work was conducted to figure out the atomization characteristics of three types of bio-diesel fuels using a common-rail injection system. The process of spray development was visualized by using a spray visualization system composed of a Nd:YAG laser and an ICCD camera, The spray tip penetrations were analyzed based on the frozen images from the spray visualization system. On the other hand, the microscopic atomization characteristics such as the distributions of SMD and axial mean velocity were measured by using a phase Doppler particle analyzer system, It is revealed that the sprays of the bio-diesel fuels have larger SMD than that of diesel fuel mainly due to high viscosity of bio-diesel. Different characteristics of bio-diesel fuels were also measured in spray tip penetrations according to the fuels and mixing ration.