This book constitutes the refereed proceedings of the 11th International Conference on Discovery Science, DS 2008, held in Budapest, Hungary, in October 2008, co-located with the 19th International Conference on Algorithmic Learning Theory, ALT 2008. The 26 revised long papers presented together with 5 invited papers were carefully reviewed and selected from 58 submissions. The papers address all current issues in the area of development and analysis of methods for intelligent data analysis, knowledge discovery and machine learning, as well as their application to scientific knowledge discovery. The papers are organized in topical sections on learning, feature selection, associations, discovery processes, learning and chemistry, clustering, structured data, and text analysis.