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To design diesel engines with low environmental impact, it is important to link health and climate-relevant soot (black carbon) emission characteristics to specific combustion conditions. The in-cylinder evolution of soot properties over the combustion cycle and as a function of exhaust gas recirculation (EGR) was investigated in a modern heavy-duty diesel engine. A novel combination of a fast gas-sampling valve and a soot particle aerosol mass spectrometer (SP-AMS) enabled online measurements of the in-cylinder soot chemistry. The results show that EGR reduced the soot formation rate. However, the late cycle soot oxidation rate (soot removal) was reduced even more, and the net effect was increased soot emissions. EGR resulted in an accumulation of polycyclic aromatic hydrocarbons (PAHs) during combustion, and led to increased PAH emissions. We show that mass spectral and optical signatures of the in-cylinder soot and associated low volatility organics change dramatically from the soot formation dominated phase to the soot oxidation dominated phase. These signatures include a class of fullerene carbon clusters that we hypothesize represent less graphitized, C-containing fullerenic (high tortuosity or curved) soot nanostructures arising from decreased combustion temperatures and increased premixing of air and fuel with EGR. Altered soot properties are of key importance when designing emission control strategies such as diesel particulate filters and when introducing novel biofuels.