In the course of systematic radioisotopic tests of sulfided CoMo catalysts in the HDS of thiophene the effects of catalyst composition and the nature of the feed on the number, distribution and functioning of the active sites of these catalysts have been studied. A method to estimate the ratio between surface SH groups, coordinatively unsaturated sites (CUSs) and functioning vacancies in the catalyst active phase has been established. It has been shown that the CoMo catalyst activity is determined not only by the number of SH groups and their mobility, but also by the number of the vacancies for thiophene adsorption. On the basis of the obtained data, general conditions for the formation and functioning of active sites due to the nature of crude have been formulated and criteria to evaluate the efficiency of catalyst functioning have been developed. The results of pilot plant HDS tests of ten commercial CoMo catalysts have confirmed the developed criteria.