This book reports on the methods and models that were applied in the project “Pathways to Sustainable European Energy Systems”, which is a 5-year project (2006-2010) aimed at evaluating pathways to a sustainable European energy system, with a focus on the stationary energy system and the time period up to the year 2050. The results obtained during the project are reported in the book “European Energy Pathways - Pathways to Sustainable European Energy Systems” and in various scientific papers. The present energy system has been included in the analysis, as this will have a significant influence on possibilities to transform the energy system over the coming decades. Therefore, a cornerstone of the project has been the establishment of extensive databases related to the European energy infrastructure, and including the global fossil fuel infrastructure. The pathway analysis has applied a variety of energy-related methods and models that originate from different scientific disciplines and traditions. Some of the applied analytical tools are well-known, well-documented, and widely used in academic research, while others have been developed (or refined) during the Pathways project and are therefore unique. To a certain extent, the Pathways project has also served as a “testing ground” for exploring the possibilities and challenges of coordinated multi-model analyses of complex problems. The aim of this book is to give a more in-depth presentation of the project from a methodological viewpoint than that provided in the Results book. In all, some 40 researchers have been involved in the work.