Sustainable urban development has been widely recognized as requiring energy and transport efficient urban growth, while ecological issues are often not well integrated in sustainability assessments and Strategic Environmental Assessment (SEA). In order to achieve such integration, methods and tools based on Geographic Information Systems (GIS) in a Landscape Ecological Assessment (LEA) framework were developed and integrated in planning in four case studies in and around the city of Stockholm, Sweden. This involved the application of recently developed methods for impact prediction and for integration into the planning processes. The aim of the study was to compare the case studies concerning strengths and weaknesses of LEA and its GIS-based components. The methodology enabled identification of important structures in the landscape to support biodiversity, across administrative borders. The LEA facilitated discussions on consequences of alternatives for localisation of built-up areas, infrastructure and other developments as well as management. The GIS-based LEA approach could thus contribute to a sustainable urban development with consideration of the landscape-level biodiversity values integrated with energy-efficient urban growth trajectories.