Spatial analysis of pan distribution in Botswana indicates that there is a clear structural control on their distribution. SpaDiS™ plots of spatial translations indicate northeast-trending corridors, one prominent at 030° and the other of local significance at 045°; a prominent northwest-trending corridor at 130°; and a locally important north-south trend at 175°. The northwest and northeast trends coincide with a conjugate fault set recognised in Botswana, which in the northern parts of the country coincides with east-west extension related to the formation of the Okavango Rift and reactivation of structures in the basement. The north-south trend corresponds to another known fracture set in northern Botswana and also, the trend of interdune hollows in this region. Although processes such as aeolian deflation and salt weathering are important in the development of pans in Botswana, initiation of the depressions and their location is structurally controlled. We conclude that structural focusing of groundwater and neo-tectonic movements along fractures plays a critical role in pan location and development.