In the Altai-Sayan mountain region, located in southern Siberia, there are a number of caves developed in rocks in which karst processes are impossible to occur. In East Sayan, these are the Big Oreshnaya and Dudinskaya caves, the total length of which is more than 50 km and 35 km, respectively. Within the Altai Mountains, these are the Altaiskaya and Kek-Tash caves with a total length of 4.7 and 3.2 km, respectively. Mapping of the listed caves revealed that the morphology of their passages and the general structure differ significantly from those of caves in carbonate rocks. The passages have a flattened shape in cross section. Their width is usually meters and tens of meters, vertical extension is tens and hundreds of meters, and lateral extension is hundreds of meters. In general, the pattern of the passages is arranged in a box-like structure, where the pasages fit into a system of disjoint extended subvertical planes with rare short subvertical planes connecting them. The structure of the passages of the studied caves resembles the structure of karst caves, rotated vertically by 90°. The main directions of the passages there are not aligned in subhorizontal planes, but in subvertical ones. The revealed structure corresponds to the geometry of the structural pattern of Late Cenozoic fault systems formed as a result of subhorizontal compression. Signs of abundant argillization (alteration of the initial substance by hydrothermal processes and its replacement by newly formed clay minerals) were found in the studied caves. The formation mechanism of the studied caves is offered: removal of the substrate argillized by hydrothermal processes along the fault zones, by groundwater without significant participation of karst processes.