Abstract Very few researchers have focused on the question of: if and to what extent, regional economic disparities affect military base closures. In this paper, we aim to explain regional patterns of military base closures in the Czech Republic, a country that has experienced a sharp decline in military employment and expenditures since the beginning of 1990s. Three groups of predictors of closure were considered: local (size, age, location and hierarchical position of the military base); regional (wages, unemployment, city size, the initial level of militarisation of the district); and national-level predictors (geostrategic priorities and restructuring of the Czech Armed Forces). Our research is informed by the theory of public choice and its application to the decision-making processes concerning military base closures and realignments. We employed a combination of regression models to determine which group of the above-mentioned factors affected the spatial distribution of military bases in the period 1994–2005. While geostrategic factors (such as distance from the border with West Germany) and restructuring of the army (type of a military base) were the most important, regional economic disparities showed no significant correlation with the intensity of military base closures/downsizing. We did not demonstrate that military bases in economically lagging regions had been systematically protected in the Czech Republic.