The 13th International Conference on Implementation and Application of - tomata (CIAA 2008) was held at San Francisco State University, San Francisco, July 21–24, 2008. This volume of Lecture Notes in Computer Science contains the papers that were presented at CIAA 2008, as well as the abstracts of the poster papers that were displayed during the conference. The volume also includes the - per/extended abstract of the four invited talks presented by Markus Holzer, Kai Salomaa, Mihalis Yannakakis, and Hsu-Chun Yen. The 24 regular papers were selected from 40 submissions covering various topics in the theory, implementation, and applications of automata and related structures. Each submitted paper was reviewed by at least three ProgramC- mittee members, with the assistance of external referees. The authors of the papers and posters presented in this volume come from the following co- tries: Australia, Belgium, Canada, China, Columbia, Czech Republic, France, Germany, Hungary, Italy, Japan, The Netherlands, Poland, Portugal, Romania, Russia, Spain, Sweden, Taiwan, United Arab Emerates, and USA. We wish to thank all who made this conference possible: the authors for s- mitting papers, the Program Committee members and external referees (listed in the proceedings) for their excellent work, and the four invited speakers. Finally, we wish to express our sincere appreciation to the sponsors, local organizers, and the editors of the Lecture Notes in Computer Science seriesand Springer, in particular Alfred Hofmann, for their help in publishing this volume in a timely manner.