Biodiesels derived from vegetable oils present a very promising alternative for diesel fuel, since they have numerous advantages compared to fossil fuels. They are renewable, biodegradable, provide energy security and foreign exchange savings besides addressing environmental concerns and socio-economic issues. However drawbacks associated with biodiesel of high viscosity and low volatility which cause combustion problems in compression ignition engines, call for low heat rejection (LHR) engine. LHR engines have significant characteristics of higher operating temperature, maximum heat release, and ability to handle low calorific value fuel. Investigations were carried out to determine exhaust emissions with LHR engine and conventional engine (CE) with crude cotton seed biodiesel. L H R e n g i n e consisted of an air gap insulated piston, an air gap insulated liner and ceramic coated cylinder head with different operating conditions of normal temperature and preheated temperature cottonseed biodiesel with varied injector opening pressure. Nozzle testing apparatus was used to increase injector opening pressure. Particulate emissions and oxides of nitrogen were determined with sophisticated analyzers at full load operation of the engine. LHR engine reduced pollutants at higher injector opening pressure at preheated temperature of biodiesel in comparison with neat diesel operation on CE.