This book constitutes the refereed proceedings of the 11th International Conference on Implementation and Application of Automata, CIAA 2006, held in Taipei, Taiwan, in August 2006. The 22 revised full papers and 7 revised poster papers presented together with the extended abstracts of 3 invited lectures were carefully reviewed and selected from 76 submissions. The papers cover various topics in the theory, implementation, and applications of automata and related structures.