Experimental work has been carried out on a small displacement Euro 5 automotive diesel engine fueled alternatively with ultralow sulfur diesel (ULSD) and with two blends (30% vol) of ULSD, with two different fatty acid methyl esters (FAME) obtained from rapeseed methyl ester (RME) and jatropha methyl ester OME). The engine-out particulate matter (PM) emissions have been characterized in terms of number and mass size distributions; measurements were performed under different engine operating conditions that are representative of the New European Driving Cycle (NEDC), including cold start of the engine. No significant differences were detected in the particle numbers (PN) for the different fuels under steady-state operating conditions, while a moderate reduction in particle mass size distribution was observed for the biofuel blends. The effects on PN emissions due to shifts in the engine operating points on the calibration maps, caused by the different fuel characteristics, have been shown to be significantly larger than the effects due to the different combustion characteristics of the biofuel blends, thus highlighting the need for a specific adjustment of the engine calibration.