This work reports on the determination of the structure-reactivity correlation of soot using Raman microscopy (RM) and temperature programmed oxidation (TPO), as well as on changes in the emission level of polycyclic aromatic hydrocarbons (PAH) and carbonyls at the combustion of biofuels. To characterize the reactivity of soot the combustion behaviour of model- and diesel soot has been determined by means of TPO in the presence of oxygen. In this context, spark-discharge soot and graphite powder were applied as model substances, and EURO VI and IV diesel soot as real-diesel soots. The structure of soot samples was investigated by RM and structural changes during the TPO were observed. In order to make a statement about the changes in PAH and carbonyl compound emissions during combustion of biofuels, samples were taken at different engine testbenches. Fossil fuel, biodiesel and vegetable oil were used during this study, as well as fuel mixtures with different biofuel fractions.