This volume contains the papers presented at the 29th Symposium on Mat- matical Foundations of Computer Science, MFCS 2004, held in Prague, Czech Republic, August 22–27, 2004. The conference was organized by the Institute for Theoretical Computer Science (ITI) and the Department of Theoretical Com- ter Science and Mathematical Logic (KTIML) of the Faculty of Mathematics and Physics of Charles University in Prague. It was supported in part by the Eu- pean Association for Theoretical Computer Science (EATCS) and the European Research Consortium for Informatics and Mathematics (ERCIM). Traditionally, the MFCS symposia encourage high-quality research in all branches of theoretical computer science. Ranging in scope from automata, f- mal languages, data structures, algorithms and computational geometry to c- plexity theory, models of computation, and applications including computational biology, cryptography, security and artificial intelligence, the conference offers a unique opportunity to researchers from diverse areas to meet and present their results to a general audience. The scientific program of this year’s MFCS took place in the lecture halls of the recently reconstructed building of the Faculty of Mathematics and P- sics in the historical center of Prague, with the famous Prague Castle and other celebrated historical monuments in sight. The view from the windows was ach- lenging competition for the speakers in the fight for the attention of the audience. But we did not fear the result: Due to the unusually tough competition for this year’s MFCS, the admitted presentations certainly attracted considerable in- rest. The conference program (and the proceedings) consisted of 60 contributed papers selected by the Program Committee from a total of 167 submissions.