Current developments in fuels and emissions regulations are resulting in an increasingly severe operating environment for diesel fuel injection systems. The formation of deposits within the holes or on the outside of the injector nozzle can affect the overall system performance. The rate of deposit formation is affected by a number of parameters, including operating conditions and fuel composition. For the work reported here an accelerated test procedure was developed to evaluate the relative importance of some of these parameters in a high pressure common rail fuel injection system. The resulting methodology produced measurable deposits in a custom-made injector nozzle on a single-cylinder engine. The results indicate that fuels containing 30%v/v and 100% Fatty Acid Methyl Ester (FAME) that does not meet EN 14214 produced more deposit than an EN590 petroleum diesel fuel. Overall, the addition of zinc to the fuel had the biggest effect on deposit formation and resulted in a 12.2% decrease in Indicated Mean Effective Pressure (IMEP). The effects of zinc were unexpectedly reduced when it was added to fuel containing 30%v/v biodiesel. Reducing the common-rail pressure with 30%v/v biodiesel (no added zinc) increased the loss in IMEP. Raising the air and fuel temperatures by 40°C and 30°C respectively showed no bigger loss in IMEP. The results indicate that deposit formation may continue after engine shut down.