To reveal the research performance and trends of the Czech Republic, this study carried out a bibliometric analysis of Czech publications during 1993 – 2012 covered in the Science Citation Index Expanded. A total of 105,103 articles were analyzed in terms of categories, publication sources (journals), contributing institutions, countries, authors, collaboration, most cited articles, as well as research emphases by the distribution of article title words, author keywords, and KeyWords Plus. The main findings include: (a) the annual numbers of Czech articles rose almost steadily during 1993-2012, with a sudden increase in 1994 due to the split of Czechoslovakia in 1993; (b) multidisciplinary materials science, physical chemistry, and multidisciplinary chemistry were the most active research categories; (c) Czech journals were more preferred to by Czech scientists compared to the foreign journals, while the top three journals were Collection of Czechoslovak Chemical Communications, Chemicke Listy, and Czechoslovak Journal of Physics; (d) Except for the Academy of Sciences of the Czech Republic, Charles University in Prague contributed the most articles and had the highest growth rate among the top seven institutions; (e) the most frequently collaborative countries were five of seven industrial countries: Germany, United States, France, United Kingdom, and Italy, as well as the other successor of Czechoslovakia, i.e. Slovakia; (f) The Czech research related to mechanical properties, Raman spectroscopy, phylogeny, and oxidative stress have come more popular in recent years.