Fuel atomization and air-fuel mixing processes play a dominant role on engine performance and emission characteristics in a direct injection compression ignition engine. Understanding of microscopic spray characteristics is essential to predict combustion phenomena. The present work investigated near nozzle flow and atomization characteristics of biodiesel fuels in a constant volume chamber. Waste cooking oil, Jatropha, and Karanja biodiesels were applied and the results were compared with those of conventional diesel fuel. The tested fuels were injected by a solenoid injector with a common-rail injection system. A high-speed camera with a long distance microscopic lens was utilized to capture the near nozzle flow. Meanwhile, Sauter mean diameter (SMD) was measured by a phase Doppler particle analyzer to compare atomization characteristics. The experimental results showed that the biodiesels had poor macroscopic spray characteristics showing longer liquid tip penetration length and narrower spray angle than those of diesel. Based on microscopic imaging, biodiesels exhibited longer injection delay and resisted formation of ligaments compared to baseline diesel due to higher viscosity and surface tension. In addition, the estimation of SMD size revealed that biodiesels had larger SMD than that of baseline diesel. The mean injection velocity of biodiesel droplets was smaller than diesel due to higher frictional losses in the nozzle.