The rapid depletion of petroleum reserves and stringent emission legislation due to global warming has compelled us to pursue alternative fuels. Biodiesel is an alternative diesel fuel that can be produced from renewable feedstock such as edible and non-edible vegetable oils, wasted frying oils and animal fats. Biodiesel is an oxygenated, sulphur free, non-toxic, biogradable and renewable fuel. In the present study, a military 585 kW compression ignition diesel injection (CIDI) engine was fuelled with diesel, Karanja oil methyl ester (KOME) and Jatropha oil methyl ester (JOME) biodiesel respectively. These were subjected to 100 hours long term endurance tests. Lubricating oil samples drawn from engine after a fixed interval (20 hours) were subjected to elemental analysis. Metal debris concentration analysis was done by atomic absorption spectroscopy. Lubricating oil samples were also subjected to ferrography test. Wear of metals were found to be lowered for both biodiesel operated engine. Scanning electron microscopy was also conducted on the cylinder liner surfaces exposed to wear. All the tests were conducted with new set of engine parts for all test fuels. The performances of fuels were also evaluated in terms of power and heat release rates. The emission of carbon monoxide (CO), unburnt hydrocarbon (UHC), and oxides of nitrogen NOx with the three fuels were also compared. Both Karanja and Jatropha oil, after transesterification exhibit the properties within acceptable limits of ASTM standard. Engine performance with both KOME and JOME were slightly lower than diesel. Emissions performance of KOME and JOME were slightly better than diesel.