The refereed proceedings of the 9th Annual International Computing and Combinatorics Conference, COCOON 2003, held in Big Sky, MT, USA in July 2003. The 52 revised full papers presented together with 3 invited contributions were carefully reviewed and selected from 114 submissions. The papers are organized in topical sections on computational geometry, computational biology, computability and complexity theory, graph theory and graph algorithms, automata and Petri net theory, distributed computing, Web-based computing, scheduling, graph drawing, and fixed-parameter complexity theory.