This book presents the refereed proceedings of the 12th Annual International Computing and Combinatorics Conference, COCOON 2006, held in Taipei, Taiwan, August 2006. The book offers 52 revised full papers presented together with abstracts of 2 invited talks. The papers are organized in topical sections on computational economics, finance, and management, graph algorithms, computational complexity and computability, quantum computing, computational biology and medicine, computational geometry, graph theory, and more.