Material and energy flows (together with human appropriation of land) are considered the key cause of environmental problems. This paper describes the application of economy-wide material flow accounting and analysis to the economy of the Czech Republic for 1990-2002. The results show a decrease of material intensity and decoupling of the economic growth from environmental pressure. The second part of the paper treats an important issue of uncertainties related to economy-wide material flow indicators in the Czech Republic. The results point out that the high uncertainties related to some material flow indicators may be an obstacle to their applicability.