Geological structure and petroleum potential of Paleozoic in the West-Siberian oil and gas basin remains unstated and underestimated despite research projects conducted and hydrocarbon deposits discovered in Paleozoic sediments. This is attributed firstly to exploration works focused on Mesozoic oil and gas complex due to its high potential, and secondly to exiting tectonic model of the region where Paleozoic complex is included in folded basement or foundation. According to sediment migration theory of hydrocarbon generation, the basement of the basin is not a source for hydrocarbon fluids, and therefore cannot be considered as an independent oil and gas complex with its own hydrocarbon source rocks and reservoirs. However, oil and gas deposits discovered in the basement of Western Siberia show inconsistency of currently existing hypotheses and models. Among them there are two major versions for hydrocarbon origin in Paleozoic organic and inorganic theories. Geological structure and reservoir distribution in Paleozoic complexes is very specific and require a thorough analysis of all geological, geophysical and geochemical materials.