Stringent emission legislations, brought in due to global warming and rapid depletion of petroleum reserves, have given us the opportunity to find bio fuels. Biodiesel is an alternative to diesel fuel that can be produced from feedstock such as edible and non-edible vegetable oils, bio-mass, wasted frying oils and animal fats. Biodiesel is green, renewable, sulphur free, non-toxic, and oxygenated biogradable fuel. Jatropha and Karanja oils are non- edible vegetable oils. Jatropha and Karanja biodiesel are prepared using methanol by the process of transesterification. JOME and KOME biodiesel were found to be highly compatible alternative fuels. JOME and KOME have comparable performance with low emission characteristics, except for NOx emission, in comparison to diesel fuel. Most recent emission legislations also restrict the total number of nano particles emitted in addition to particulate matter, due to the adverse health impact. In the present study, performance, combustion and emissions of CO, CO2, UHC, NOx and PM including particle size-numbers distribution characteristics, were compared for JOME, KOME and diesel fuels by applying EGR with turbo charging, in a 12 cylinders, 720 kW, 38.8 liters CIDI military diesel engine. The test results showed that engine performance with both KOME and JOME biodiesel fuels were slightly lower than with diesel fuel. Both biodiesel fuels, with 20% EGR rate, have produced lower exhaust emissions including 21-24% lower NOx emission along with lower particulate size-number distribution, particle size-surface area distribution and total particulate number concentration, as compared to diesel fuel with 20% EGR rate.