This book constitutes the refereed proceedings of the 6th International Workshop on Data Integration in the Life Sciences, DILS 2009, held in Manchester, UK, on July 20-22, 2009. The 15 revised papers included in this volume together with 2 invited papers were carefully reviewed and selected. The papers cover the following topics: graph-based modelling and integration, annotation, structure inference, data and work flows, data integration for systems biology. The workshop brings together results on a collection of different strands of data integration research, in particular reflecting the evolving nature of biological data sources and integration requirements.