Chronic conditions contribute to the majority of the mortality and morbidity burden in Europe. The extent to which infectious agents are responsible for the chronic disease burden remains elusive. The complex nature of the natural history of chronic conditions calls for an overview of ongoing research activities linking infectious agents with these conditions in order to guide research endeavours, direct research funding, steer prevention efforts, and point health policy towards promising interventions. A selection of websites hosted by institutions either financing or conducting research within the European Union was screened for ongoing research activities examining infectious aetiology of chronic conditions. The searches were conducted until September 2011, applying search strategies and inclusion criteria predefined in a study protocol. In total, 25 research activities met the inclusion criteria. Of those, ten activities were focused to investigate infectious aetiology of cancer, four focused on type 2 diabetes mellitus, and 11 focused on a wide spectrum of other chronic conditions. The identified research projects did not cover areas such as mental and behavioural disorders. Infectious agents analysed included enteroviruses, Epstein-Barr virus, human rhinoviruses, P. gingivalis, human papillomaviruses, cytomegalovirus, Helicobacter spp. and human parvovirus. Only three projects specifically addressed therapeutic interventions. Ultimately, linking infectious agents with chronic conditions may translate into prevention efforts with vaccinations or treatment strategies with antimicrobial agents, and could, thus, eventually reduce the heavy disease burden from chronic conditions. However, little translational research on therapeutic interventions was found in our search and should be fostered, particularly for more established infectious-chronic disease associations.