This work investigates the effect of a multifunctional diesel fuel additive package used with RapeSeed Oil (RSO) as a fuel in a DI heavy duty diesel engine. The effects on fuel injectors’ cleanliness were assessed. The aim was to maintain combustion performance and preventing the deterioration of exhaust emissions associated with injector deposit build up. Two scenarios were investigated: the effect of deposit clean-up by a high dose of the additive package; and the effect of deposit prevention using a moderate dose of the additive package. Engine combustion performance and emissions were compared for each case against use of RSO without any additive. The engine used was a 6 cylinder, turbocharged, intercooled Perkins Phaser Engine, fitted with an oxidation catalyst and meeting the Euro II emissions limits. The tests were conducted under steady state conditions of 23kW and 47kW power output at an engine speed of 1500 rpm. The in-cylinder pressure, gaseous and particulate exhaust emissions were measured. The injectors were inspected using SEM (Scanning Electronic Microscopy). The results show that the use of the multifunctional fuel additive package reduces the ignition delay (ID), increases the premixed combustion duration (PCD) and improves the combustion stability. The multifunctional fuel additive package also reduced the deposit build up on the fuel injectors and prevented the deterioration of engine-out particulate, CO and hydrocarbon emissions