This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003.The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.