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This book constitutes the thoroughly refereed post-proceedings of the 9th International Workshop on DNA Based Computers, DNA9, held in Madison, Wisconsin, USA in June 2003.The 22 revised full papers presented were carefully selected during two rounds of reviewing and improvement from initially 60 submissions. The papers are organized in topical sections on new experiments and tools, theory, computer simulation and sequence design, self-assembly and autonomous molecular computation, experimental solutions, and new computing models.