This volume contains the papers presented at the 13th International Symposium on String Processing and Information Retrieval (SPIRE), held October 11-13, 2006, in Glasgow, Scotland. The SPIRE annual symposium provides an opportunity for both new and established researchers to present original contributions to areas such as string processing (dictionary algorithms, text searching, pattern matching, text c- pression, text mining, natural language processing, and automata-based string processing); information retrieval languages, applications, and evaluation (IR modelling, indexing, ranking and ?ltering, interface design, visualization, cro- lingual IR systems, multimedia IR, digital libraries, collaborative retrieval, W- related applications, XML, information retrieval from semi-structured data, text mining, and generation of structured data from text); and interaction of biology and computation (sequencing and applications in molecular biology, evolution and phylogenetics, recognition of genes and regulatory elements, and sequen- driven protein structure prediction). The papers in this volume were selected from 102 papers submitted from over 20 di?erent countries in response to the Call for Papers. A total of 26 submissions were accepted as full papers, yielding an acceptance rate of about 25%. In view of the large number of good-quality submissions the Program Committee decided to accept 5 short papers, that have also been included in the proceedings. SPIRE 2006 also featured two talks by invited speakers: Jamie Callan (Carnegie Mellon University, USA) and Martin Farach-Colton (Rutgers University, USA).