In our contribution, we estimate the output gap that is consistent with a fully specified DSGE model. The output gap is defined in this framework as a deviation of actual output from its flexible-price equilibrium level. The flexible-price equilibrium corresponds to the state of the economy with more efficient allocation. These estimates are thus useful indicators for monetary policy. Our output gap illustrates Czech business cycles which are rather different to other estimates (e.g. HP filter). This result may be typical for economies in transition. Moreover, our results for the Czech economy show that the turning points in the gaps are accompanied by government changes.