The article presents results of the study devoted to evolution of science and technology system in Czech Republic (CR) during the transformation period (from the victory of the velvet revolution in 1989 till 2004, when CR joined the EU). Peculiarities of transformations in CR at various transformation stages are shown on the basis of official statistics, expert opinion and survey data, and by methodology elaborated in the international project 'Restructuring and Reintegration of Science & Technology Systems in Economies in Transition'. Science & technology and innovation position of CR against other post-socialist countries of Central Europe and South European countries is shown by use of indicators included in the European Innovation Scoreboard. The conclusion is that CR which immediately took a 'rigid' course toward the reconstruction of national science & technology system (NSTS) by the criteria of Western European model, had a good chance to achieve the goal on the eve of joining the EU, as CR could quite successfully transform some of the key parameters of NSTS, especially those related with the research segment (although technological losses were also notable). The weakest side of science & technology transformation in CR in 90s proved to be setting up the horizontal links within the national innovation system. However, official statistics of CR (2000-2004) shows a positive dynamics of R&D parameters in the private sector, which is an indicator of rehabilitating trends in the innovation segment of this country on the eve of its joining the EU.