Municipal indebtedness has become a much debated issue in recent years. This paper analyzes debt development and structure for all the municipalities in the Czech Republic for the years 2001–2014 and examines the indebtedness of a selected sample of municipalities. The paper also evaluates the tools currently available to regulate municipal indebtedness. The methods and procedures used by the authors mainly involve research in professional literature and the analysis of available data on municipal indebtedness. The analysis was concerned primarily with municipalities that have been assessed in recent years as municipalities with a higher rate of economic risk by the Municipal Financial Management Monitoring system performed by the Ministry of Finance of the Czech Republic. The completed analysis suggests that municipal indebtedness is not high when compared to the public debt of the Czech Republic. Only a few municipalities are dealing with indebtedness (or over-indebtedness). Large cities are capable of fulfilling their financial obligations.