Relevance. The results of paleontological, geophysical, and mineragraphic studies of flints in Artinskian stage deposits in the Cis-Urals are presented. Purpose of the work. Reef organogenic structures with silicified limestones and flints, silicified sandstones and injections of flints into them have been studied. The goal is to show the hydrothermal nature of chert injections into reefs and sandstones. Research methods. Geophysical electrical prospecting studies of reef limestones with the aim of identifying areas of silicification, geological and paleontological mapping of reefs, biostromes, bioherms, sandstones, areas of accumulation of nodules and flint nodules, study of polished sections of silicified rocks, production of thin sections and their mineragraphic study. Results of the work. Paleontological mapping of the reef structure made it possible to establish the different species composition, size, and preservation of biota in the coastal, summit and outer parts of the reef. Mineragraphic studies have established the high-temperature hydrothermal nature of chert in all types of sediments. Hydrothermal injections of chert into sandstone layers occur by diffusion with the formation of siliceous nodules and Lysigang rings in sandstones. Intensive penetration of silicon hydrotherms into sandstone layers forms areas of silicification in them in the form of laccoliths tens of meters in size. Various degrees of development of flint hydrotherms by marine fauna have been established. Flints may include small specimens of small fauna, be rich in well-preserved fauna, or include layers of biota overlain by layers of flints covered with new colonies of microorganisms. Sometimes cherts contain only fragments of faunal shells caught in the hot gel of cherts. Conclusions. Hydrotherms of siliceous composition in loose marine sediments could be a condition for the development of biota and the basis for reef structures. Increased values of electrical resistivity of flints and silicified limestones allow electrical prospecting to explore the internal structure of reefs. It has been suggested that in the Carboniferous and Early Permian in the Cis-Urals there was a hydrothermal belt extending from Kungur to Sterlitamak.