The effects of biodiesel oxidation stability on diesel fuel injection equipment (FIE) behavior were investigated using newly developed test rig and methodology. On the test rig, biodiesel blend fuels were circulated through a fuel tank and a common rail injection system. Fuel injected from typical diesel injectors was returned into the fuel tank to enhance the speed of fuel degradation. The results showed that injector deposits could be reproduced on a test rig. It was observed that injector body temperature increase accelerates the degradation of fuel and therefore gives earlier FIE failure. Fuel renewal could partially restore the injection quantity after complete failure at low injection pressure, thus showing a potential cleaning effect on injector deposits when refueling a car. Fuel quality was monitored during the rig test to investigate the degradation trends and it was seen that there are two major steps during fuel deterioration: an oxidation followed by an acidification together with increasing water content inside the fuel.