This work focuses on the impact of fuel on soot reactivity and nanostructure. A 2.5L, 4-cylinder, turbocharged, common rail, direct injection light-duty diesel engine was used in generating soot samples. The engine was operated at 2400 rpm and 64 Nm. Three test fuels have been used: an ultra low sulfur diesel fuel (BP15), a pure soybean methyl-ester (B100), and a synthetic, particularly free of sulfur and aromatic compounds, Fischer-Tropsch fuel (FT) produced in a gasto- liquid process. The start of injection (SOI) and fuel rail pressures have been adjusted such that the three test fuels have similar combustion phasing. The reactivity of soot samples was investigated by thermogravimetric analysis (TGA). According to TGA, B100 soot exhibits the fastest oxidation on a mass basis with BP15 and FT soot in order of oxidation rate. Crystalline information for the soot samples was obtained using X-ray diffraction (XRD). XRD results show that B100 soot has the smallest average number of stacking layers, while FT soot has the longest basal plane diameter. TEM was used to obtain images of the graphene layers, and a quantitative image analysis algorithm has been developed. B100 soot has the shortest mean fringe length and greatest mean fringe tortuosity. The characterization results suggest a relation between soot reactivity and nanostructure: the higher degree of structural disorder is related to the faster oxidation rate of diesel soot even for B100 soot, which is consistent with past work by Vander Wal and co-workers, but in contrast to past work by Boehman and co-workers which identified surface oxygen content as the primary explanation for increased oxidative reactivity.