This book constitutes the refereed proceedings of the 13th International Scandinavian Symposium and Workshops on Algorithm Theory, SWAT 2012, held in Helsinki, Finland, in July 2012, co-located with the 23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012. The 34 papers were carefully reviewed and selected from a total of 127 submissions. The papers present original research and cover a wide range of topics in the field of design and analysis of algorithms and data structures.