► The formation of PAH in low temperature pyrolysis was investigated for diesel fuel, surrogate diesel fuels and 13C labelled PAH. ► A thermal pyrolysis flow reactor connected to a GCMS was used to analyse the products. ► The PAH compounds produced were identified and the routes arising from the thermal decomposition of hexadecane and methyl palmitate were modelled. A study has been made of the formation of PAH from biodiesel and conventional diesel fuel using a flow cell reactor at temperatures of 600–900°C. The reaction mechanism has been validated by modelling studies using Chemkin. Pyrolysis of 9-13Cmethylphenanthrene was undertaken to investigate the demethylation reaction of methyl-PAH compounds present in the original petroleum diesel. The product profiles obtained are shown to be similar for all fuels studied, pointing to a commonality of mechanism after the decomposition of the parent hydrocarbon. Dealkylation was demonstrated as the main reaction using the 9-13Cmethylphenanthrene, however other 13C labelled species were also formed.