The main goals of European Union, expressed in its political documents on energy policy are to establish a common energy system that is sustainable with respect to reducing greenhouse gas emissions and to improve the security of energy supplies to Europe. A pan-European energy infrastructure is seen as an essential enabler. The European Academies Science Advisory Council (EASAC) was established in 2001 by the national science academies of the EU member states to provide independent advice to EU policy makers on the science underpinning a key policy decisions. Article summarized the energy systems integration issues, addressed in studies undertaken by EASAC over the last years and draws some cross-cutting conclusions on the challenges associated with the analysis, designs and operation of integrated energy systems and how they may be met. A better understanding is needed of systems dynamics, transitions, integration and how the system as a whole works. Systems approaches must take into account the reception and integration of new technologies into society.