This book constitutes the refereed proceedings of the 31st International Symposium on Mathematical Foundations of Computer Science, MFCS 2006. The book presents 62 revised full papers together with the full papers or abstracts of 7 invited talks. All current aspects in theoretical computer science and its mathematical foundations are addressed, from algorithms and data structures, to complexity, automata, semantics, logic, formal specifications, models of computation, concurrency theory, computational geometry and more.