This book constitutes the thoroughly refereed post-proceedings of the 9th International Conference on Implementation and Application of Automata, CIAA 2004, held in Kingston, Canada in July 2004. The 25 revised full papers and 14 revised poster papers presented together with 2 invited contributions have gone through two rounds of reviewing and improvement. The topics covered range from applications of automata in natural language and speech processing to protein sequencing and gene compression, and from state complexity and new algorithms for automata operations to applications of quantum finite automata.