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The article deals with modern econometric methods that will be used in long-term structural macro econometric modeling of the Czech economy. The structural model is estimated for the Czech economy to quarterly data 2005Q1 -2016Q4. On the basis of the economic theory is to derive long-term relationships for a small open economy with 9 endogenousvariables (6 domestic and 3 international) and 1 exogenous variable. The data source was the Eurostat database, FRED, Czech National Bank and the Czech Statistical Office.This article aims to find cointegration equations for modeling the long-term equilibrium of economic relations in the Czech Republic in the analyzed period. Based on the number of determined cointegration relationships is tested weak exogenous and there are tested hypotheses considering by restrictions on the coefficients so that the estimated cointegration relations in accordance with the economic and statistical theories. Achieved empirical results are influenced by the fact that the Czech economy has undergone in the period currency crisis. The calculations used EViews software version 9.