The effect of pre-catalyst speciation on lean NOx catalysis was investigated using a chemically defined fuel matrix. Nine model fuels and a diesel fuel were injected into the exhaust stream of a medium duty diesel engine prior to a DeNOx catalyst. NOx conversions ranged from 9% at a mid speed and load test point to 43% at a higher load test point. On an absolute basis, model fuels produced up to 34% greater NOx conversions relative to diesel. Speciation revealed that, compared with low temperature test points, cracking and oxidation at peak torque significantly modified the auxiliary HC input to the catalyst. The quantity of ‘cracked’ derivatives of the auxiliary fuel, namely alkene and carbonyl species, correlated well with NOx conversions.