When applying high amount of EGR (exhaust gas recirculation) in Partially Premixed Combustion (PPC) using diesel fuel, an increase in soot emission is observed as a penalty. To better understand how EGR affects soot particles in the cylinder, a fast gas sampling technique was used to draw gas samples directly out of the combustion chamber in a Scania D13 heavy duty diesel engine. The samples were characterized on-line using a scanning mobility particle sizer for soot size distributions and an aethalometer for black carbon (soot) mass concentrations. Three EGR rates, 0%, 56% and 64% were applied in the study. It was found that EGR reduces both the soot formation rate and the soot oxidation rate, due to lower flame temperature and a lower availability of oxidizing agents. With higher EGR rates, the peak soot mass concentration decreased. However, the oxidation rate was reduced even more. This led to increased soot mass concentrations with increasing EGR in late expansion and in the exhaust. During the combustion cycle, both particle number concentrations and particle mean diameters initially increased, followed by a decrease after the peak in soot mass. Generally, increasing EGR reduced the in-cylinder particle mean diameter but increased particle number concentrations. Therefore, increased particle number concentrations were the main reason for increased soot mass emissions with increasing EGR.