The paper deals with an estimate and analysis of the value of regional net fixed capital stock and the age structure of machinery and equipment in Czech agriculture. In order to perform such analysis, the official model of perpetual inventory method is transformed into the Markov chain model and applied on regional data separately. Regional net fixed capital stock is presented for the period of 2008-2013. The development of the average age of machinery and equipment comprises a potential indicator of the modernisation process in the industry. The analysis of the age structure is based on the structure heterogeneity indicator. For these purposes, the real age structure in each Czech region is compared with the theoretical stable and stationary structure. Currently, the most heterogeneous age structure of machinery and equipment occurs in Prague and the Karlovy Vary region.