This volume contains the papers presented at RECOMB 2009: the 13th Annual International Conference on Research in Computational Molecular Biology held in Tucson, Arizona, USA, during May 18-21, 2009. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner, and Michael Wat- man. RECOMB 2009 was hosted by the University of Arizona, organized by a committeechairedbyJohnKececioglu,andtookplaceatTheWestinLaPaloma Resort and Spa in Tucson, Arizona. This year, 37 papers were acccepted for presentation out of 166 submissions. The papers presented were selected by the Program Committee (PC) assisted by a number of external reviewers. Each paper was reviewed by three members of the PC, or by external reviewers acting as sub-reviewers to members of the PC. Following the initial reviews, there was an extensive Web-based discussion over a period of two weeks, leading to the ?nal decisions. The RECOMB c- ference series is closely associated with the Journal of Computational Biology, which traditionally publishes special issues devoted to presenting full versions of selected conference papers. RECOMB 2009 invited several distinguished speakers as keynotes and for a special session on Personalized Genomics . Invited speakers included C- los D. Bustamante (Cornell University), Rade Drmanac (Complete Genomics), Mark Gerstein (Yale University), Eran Halperin (Navigenics), Michael Hammer (University ofArizona),JoannaMountain(23andMe),Stephen Quake(Stanford University), Mostafa Ronaghi (Illumina), Pardis Sabeti (Harvard University), and Michael Snyder (Yale University).