This book constitutes the refereed proceedings of the 16th Annual European Symposium on Algorithms, ESA 2008, held in Karlsruhe, Germany, in September 2008 in the context of the combined conference ALGO 2008. The 67 revised full papers presented together with 2 invited lectures were carefully reviewed and selected: 51 papers out of 147 submissions for the design and analysis track and 16 out of 53 submissions in the engineering and applications track. The papers address all current subjects in algorithmics reaching from design and analysis issues of algorithms over to real-world applications and engineering of algorithms in various fields. Special focus is given to mathematical programming and operations research, including combinatorial optimization, integer programming, polyhedral combinatorics and network optimization.