While there are typically plenty of estimates of structural unemployment rate for an economy as a whole, the analysis of this phenomenon at the regional level is rather sparse. Of course, the task is quite different as the concept of structural unemployment as an image of the medium-run or long-run equilibrium of the economy does not need to hold at a regional level. This paper proposes an econometrical approach based on the search theory of the labor market. The generalized method of moments is employed to estimate the so-called stationarized unemployment rates in the fourteen regions of the Czech economy. By comparing the estimates and actually observed levels of unemployment rates, the effects of economic upswings and recessions after the year 2000 may be analyzed. Indeed, from the regional perspective the economic impacts differ substantially in certain periods of time.