This paper deals with the regional input-output analysis and its application to evaluation of the macroeconomic impact of expenditures on higher education. Regional input-output tables represent newly developed tool which can be used for the assessment of the regional economic impact of the particular industry and its institutions. The regional input-output tables were experimentally constructed by the Department of Economic Statistics at the University of Economics for all 14 Czech regions. Employing them, we can demonstrate the impact of expenditures on higher education on the macro-economic indicators and employment. This paper deals with 1 billion Czech crowns expenditures on higher education sent by the Ministry to the hypothetical higher education institution. Finally, the impact of higher education expenditures is compared with the impact of expenditures to another industries (ICT, R&D and tourism).