To study the morphological characteristics of the largest canyons in the Southern and Central Basins of Lake Baikal, we analysed a digital relief model based on high-resolution multibeam bathymetric surveying. We evaluate the role of tectonic, lithological and climatic controlling factors in the formation and evolution of canyons. Tectonic activity and seismicity act as a catalyst for canyon formation and for the development of sublacustrine gravity flows and turbidity currents, and alter the morphological appearance of already existing canyons. The influence of tectonics on the formation of the Baikal canyons is particularly noticeable on the western slope of Lake Baikal, where canyons are mainly located along faults and follow their directions. Gravity flows and turbidity currents become more important during earthquakes and periods of lower lake level. When canyon heads are located close to river mouths, riverine processes have a significant impact on the evolution of the canyon. The topography of the original surface and the lithology of the substrate also play a significant role in the evolution of canyons and in shaping the canyon morphology. During periods of lower lake level (during Pleistocene glacial periods) riverine processes were responsible for initiating the formation of many canyons in Lake Baikal. The canyons developed under the complex influence of the factors considered. One or another factor could be dominant at different stages of their evolution, while the role of the other factors became secondary. These roles could interchange over time. The Baikal canyons show a great deal of resemblance to canyons in marine environments, in terms of morphological characteristics as well as of canyon-forming processes. We propose a morphogenetic classification of the underwater valleys and canyons of Lake Baikal.