This paper aims to understand the reactivity of different nitrogen species during the catalytic hydrodenitrogenation (HDN) of a mixture of straight-run gas oil and coker gas oil. Effluents at different HDN conversions were analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS), with electrospray ionization (ESI). Positive ESI (ESI(+)) allows a selective ionization of basic nitrogen compounds, whereas negative ESI (ESI(-)) leads to selective ionization of neutral nitrogen compounds. FT-ICR/MS in ESI(+) or (-) mode generates distributions of the nitrogen compounds in the basic and neutral class, respectively, according to their carbon number and double bond equivalent (DBE), which is related to the degree of aromaticity and the number of rings. The evolution of the DBE distribution and the carbon number distribution as a function of HDN conversion gives rich information concerning the main reaction pathways and the reactivity of different nitrogen species. For the basic compounds, a shift to a lower DBE was observed, which was interpreted as the formation of partially hydrogenated or ring-opened intermediates. These intermediates were then slowly converted to the final HDN products. At intermediate conversion levels, especially light compounds were accumulated as intermediates whereas the heavy compounds were directly converted to HDN products, probably due to preferential adsorption. The neutral compounds showed a very different behavior. At the early reaction stages, they were quickly converted to HDN products, but at high conversion, the conversion of residual carbazole and tetrahydrobenzocarbazole compounds was completely inhibited. The inhibition was probably provoked by the formation of partially hydrogenated basic intermediates, which were stronger inhibitors than the aromatic pyridine rings in the feed. The contribution of cracking reactions was weak, since the overall carbon number distribution of the nitrogen compounds did not change much during hydrotreatment.