This book constitutes the refereed proceedings of the Third International Conference on Combinatorial Optimization and Applications, COCOA 2009, held in Huangshan, China, in June 2009. The 50 revised full papers were carefully reviewed and selected from 103 submissions. The papers feature original research in the areas of combinatorial optimization - both theoretical issues and and applications motivated by real-world problems thus showing convincingly the usefulness and efficiency of the algorithms discussed in a practical setting.