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- terScienceandMathematicalLogic(KTIML)oftheFacultyofMathematicsand 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- plexitytheory, modelsofcomputation, andapplicationsincludingcomputational biology, cryptography, security and arti?cial intelligence, the conference o?ers a unique opportunity to researchers from diverse areas to meet and present their results to a general audience. The scienti?c 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 celebratedhistoricalmonumentsinsight.Theviewfromthewindowswasach- lengingcompetitionforthespeakersinthe?ghtfortheattentionoftheaudience. 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.