This study investigates particulate matter (PM) and regulated emissions from renewable rapeseed oil methyl ester (RME) biodiesel in pure and blended forms and contrasts that to conventional diesel fuel. Environmental and health concerns are the major motivation for combustion engines research, especially finding sustainable alternatives to fossil fuels and reducing diesel PM emissions. Fatty acid methyl esters (FAME), including RME, are renewable fuels commonly used from low level blends with diesel to full substitution. They strongly reduce the net carbon dioxide emissions. It is largely unknown how the emissions and characteristics of PM get altered by the combined effect of adding biodiesel to diesel and implementing modern engine concepts that reduce nitrogen oxides (NOx) emissions by exhaust gas recirculation (EGR). Therefore, the exhaust from a single-cylinder Scania D13 heavy-duty (HD) diesel engine fuelled with petroleum-based MK1 diesel, RME, and a 20% RME blend (B20), was sampled while the inlet oxygen concentration was stepped from ambient to very low by varying EGR. Regulated gaseous emissions, mass of total black carbon (BC) and organic aerosol (OA), particle size distributions and the soot nanostructure by means of transmission electron microscopy (TEM), were studied. For all EGR levels, RME showed reduced BC emissions (factor 2 for low and 3-4 for higher EGR) and total particulate number count (TPNC) compared with diesel and B20. B20 was closer to diesel than RME in emission levels. RME opens a significant possibility to utilise higher levels of EGR and stay in the region of low NOx, while not producing more soot than with diesel and B20. Adding EGR to 15% inlet O2 did not affect the nanostructure of PM. A difference between the fuels was noticeable: branched agglomerates of diesel and RME were composed of many primary particles, whereas those of B20 were more often “melted” together (necking).