The aim of this work is to propose a better understanding of ultra deep HDS for diesel, to contribute to the development of advanced catalysts. The characterization of catalyst structure was examined by XRD, TPR, TPS and Raman spectroscopy. The ranking of catalytic activities were tested using various model compounds, such as thiophenes and dibenzothiophenes. The catalyst with higher stacking type active phase has weaker interaction with the support and can maintain high metal dispersion at higher metal loading. This catalyst is highly active especially for the hydrogenation pathway, which is dominant for the HDS of the most refractory sulfur compound (4,6-dimethyldibezothiophene). Not only the intrinsic HDS activity, but also the inhibiting effects by competitive adsorption of H2S and nitrogen compounds (carbazoles) need to be taken into account. From the results of systematic model reactions, NiMo catalyst is more susceptible to H2S than CoMo catalyst. The hydrogenation pathway is more strongly inhibited by nitrogen compounds than the direct desulfurization pathway, probably because of their stronger basicity. Moreover, new highly active catalyst of Ni, Mo, W supported by alumina with added titania was developed for the HDS of 4,6-dimethyldibezothiophene. It was also confirmed by the test using diesel fuel. The promising catalyst with higher hydrogenation activity tends to be susceptible to H2S and nitrogen compounds. Therefore, the process consisting of two stage reactors, containing a H2S stripper between two HDS reactors to reduce H2S pressure in the second reactor, and sequentially swing adsorbers to reduce basic nitrogen compounds was suggested.