Suitability of the compression ignition engine for biodiesel fuel based operation has been discussed in several studies. However, studies focusing on the physical characterization of exhaust particulates from engine operating with bio-diesel blends are limited. This study characterizes the particulate emissions in terms of particle size distribution from a compression ignition engine operating on diesel and bio-diesel of two different origins namely Jatropha and Karanja in the form of 20% blends, as a function of loading. A ten-stage inertial impactor (MOUDI) was used to obtain particle size distributions. It was observed that particle mass concentrations of sub-micron particles are higher for higher loading conditions. Further, test results indicated that contribution of PM2.5 particles to the exhaust to the total particulate mass varied from 75% to 95% for the load conditions used in the study.