Rapid depletion of petroleum crude oil reserves,stringent pollution legislations and global warming, has given us the opportunity to work on bio fuels. Biodiesel can be produced from edible and non-edible vegetable oils,waste bio mass and animal fats.Biodiesel is renewable,bio gradable,sulphur free, non-toxic, oxygenated and green alternative fuel. Karanja and Jatropha oils are non- edible vegetable oils. Karanja and Jatrophaoil methyl ester biodiesel are prepared by transesterification process, using methanol. JOME and KOME have comparable performance with low gaseous emission characteristics, except higher NOx emission, in comparison to mineral diesel fuel. Recent emission legislations also restrict nano particle emission in addition to particulate matter, due to their adverse impact on health.In the present study, performance, combustion and emissions of CO, CO2, UHC, NOx and PM including nano particle emission characteristics, along with engine wear were compared for KOME, JOME and