This volume contains 25 peer-reviewed papers based on the presentations at the 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008) held at the Teikyo Hotel, Zeuten Lake, near Berlin, from June 9 to June 10, 2008. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions: Boston (Gary Benson) - Graduate Program in Bioinformatics, Boston University; Berlin (Herman-Georg Holzhutter) - The International Research Training Group (IRTG) Genomics and Systems Biology of Molecular Networks; and, Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) - Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.