In this paper we analyze the geological structure and prospects of hydrocarbon potential of the Paleozoic deposits in southeastern regions of West Siberia, including the Tomsk, Novosibirsk, Omsk regions and the south-west of the Krasnoyarsk Territory in the left-bank part of the Yenisei River. In the process of our studies, we analyzed the tectonic structure of the basement and made a conclusion that most of the studied area is occupied by the Central West Siberian zone of Late Hercynides. In the northeast of the Tomsk region and the adjacent area of the Krasnoyarsk Territory, the cis-Yenisei Upper Protezoic-Paleozoic sedimentary subbasin, lying on the pre-Baikal basement, developed. We constructed regional-zonal models of the Riphean-Cambrian deposits of the cis-Yenisei subprovince and Paleozoic deposits in the area of distribution of Hercynides and analyzed the material composition and age of the rocks of the pre-Jurassic basement. We assessed hydrocarbon potential of the Upper Proterozoic-Paleozoic deposits, identified prospective blocks and objects, developed seismogeological criteria to identify and map in detail the Paleozoic oil and gas prospective reservoirs and constructed seismogeological models of reference fields.