This study investigates the morphology and nanostructure of soot particles during cold-start and hot-start engine operation of a diesel engine using oxygenated fuels. The soot samples were analysed using transmission electron microscopy. The oxygen content in the fuel was varied between 0 and 12%. The results showed that the primary particles during cold-start have significantly smaller size when compared to hot-start engine operation. The addition of oxygenated fuels also resulted in smaller sized primary particles. Smaller radius of gyration and higher fractal dimension of soot aggregates during cold-start would mean smaller aggregate size with a more compact structure. Shorter fringes with a higher inter-fringe spacing for cold-start would mean lower graphitisation of soot particles that could be related to higher oxidation reactivity of soot particles.