This book constitutes the refereed proceedings of the Third International Workshop on Data Integration in the Life Sciences, DILS 2006, held in Hinxton, UK in July 2006. The 19 revised full papers and 4 revised short papers presented together with 2 keynote talks were carefully reviewed and selected from 50 initial submissions. All current issues in data integration from the life science point of view are adressed. The papers are organized in topical sections on data integration, text mining, systems, potpourri, short papers, and workflow.