Due to the need to reduce the use of fossil fuels, renewable fuels such as biodiesels are of interest. Biodiesels have different properties to pure diesel especially higher viscosity. This research studied the effect of using biodiesel on common-rail injection nozzles. Pure diesel and two biodiesel blends were supplied to the nozzles using a 1,800 bar injection pump with the same rotational speed of 2,200 rpm for 1,000 hours. The biodiesel blends were 5% palm oil based fatty acid methyl esters (FAME) biodiesel blended with 95% diesel (B5), and 10% palm oil based FAME biodiesel blended with 90% diesel (B10). Comparing with the petroleum-derived diesel (petrodiesel) fuel, the use of higher viscosity fuels such as B5 or B10 did not show the possibility to cause wearing around the injection nozzle holes. On the other hand, the results obtained by the Scanning Electron Microscope (SEM) demonstrated that the contaminations were observed around the holes when the nozzle were tested with B5 and B10. Using the Energy Dispersive X-ray (EDX) analyzer, we expect the contaminations to be black carbon particulate, iron oxide and the tested fuels.