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This article aims to investigate the long-run structural cointegrated VAR model that relates to the core macroeconomic variables of the Czech economy to current and lagged values of a number of key foreign variables (6 domestic and 3 international) and 1 exogenous variable. This article aims to find cointegration equations for modeling the long-term equilibrium of economic relations in the Czech Republic in the analyzed period. Five long-run relationships are identified. The model includes purchasing power parity in relative version, money demand, a gap between domestic and foreign product, interest rate parity, Fisher inflation parity. A cointegration analysis showed that long-run structural equilibrium relationships correspond with empirical cointegration relationships, so the model used is suitable for a small open economy. Achieved empirical results are influenced by the fact that the Czech economy has undergone a currency crisis. The calculations used eViews software version 9. The structural model is estimated for the Czech economy. The data used have the character of a quarterly time series in the period from Q1/2005 to Q4/2016. The data source was the Eurostat database, FRED, Czech National Bank and the Czech Statistical Office.