The goal of our contribution is to find possible changes in the Czech economy in the last fifteen years. We are concerned with the questions of stability of the relationships among the key economic variables. These relationships are expressed particularly by the dynamic Okun's law, Phillips curve, IS curve or the Taylor's rule. The cyclical development of the economy is based on the simultaneous estimation of the four (unobserved) natural rates: potential output, NAIRU, equilibrium real interest rate and equilibrium real exchange rate. Unlike the mainstream (DSGE) models we use an alternative, non general equilibrium model without any strong restrictions on the parameter and model equations. Our results (among others) show that the significant changes of parameters are identified only in the period of the last economic downturn beginning the fourth quarter 2008 and that these changes influenced only a part of the key model parameters.