The effect of Si/Al ratio of zeolite Y on the performance of NiW catalysts for second stage hydrocracking was studied. The zeolites were characterized by IR spectroscopy of adsorbed pyridine, low-temperature N2 adsorption, and temperature-programmed desorption of ammonia. The observed decrease of Bronsted and Lewis acid sites concentration relates to the increase of Si/Al ratio in zeolites. According to HRTEM and XPS, sulfide component of catalysts differs in morphology, NiWS phase content and tungsten sulfidation degree. The catalysts were tested in hydrocracking of model (squalane) and real feedstock (unconverted oil (UCO) from two-stage industrial hydrocracker) at different temperatures. The increase of Si/Al ratio in zeolites was found to result in the decrease of catalytic activity and the increase of selectivity to middle distillates. However, similar selectivity of 52 and 53% at the 50% of UCO conversion was observed for catalysts containing zeolites with Si/Al ratio 24 and 37 respectively. This can be attributed mainly to the differences in the textural properties of the zeolites. The catalyst based on amorphous silica-alumina (without zeolites) was found to have a higher selectivity to middle distillates and lower activity as compared to zeolite-based catalysts.