Background: Previous analyses concerning health components of European Union (EU)-funded research have shown low project participation levels of the 12 newest member states (EU-12). Additionally, there has been a lack of subject-area analysis. In the Health Research for Europe project, we screened all projects of the EU’s Framework Programmes for research FP5 and FP6 (1998–2006) to identify health research projects and describe participation by country and subject area. Methods: FP5 and FP6 project databases were acquired and screened by coders to identify health-related projects, which were then categorized according to the 47 divisions of the EU Health Portal (N = 2728 projects) plus an extra group of ‘basic/biotech’ projects (N = 1743). Country participation and coordination rates for projects were also analyzed. Results: Approximately 20% of the 26 946 projects (value €29.2bn) were health-related (N = 4756. Value €6.04bn). Within the health categories, the largest expenditures were cancer (11.9%), ‘other’ (i.e. not mental health or cardiovascular) non-communicable diseases (9.5%) and food safety (9.4%). One hundred thirty-two countries participated in these projects. Of the 27 EU countries (and five partner countries), north-western and Nordic states acquired more projects per capita. The UK led coordination with > 20% of projects. EU-12 countries were generally under-represented for participation and coordination. Conclusions: Combining our findings with the associated literature, we comment on drivers determining distribution of participation and funds across countries and subject areas. Additionally, we discuss changes needed in the core EU projects database to provide greater transparency, data exploitation and return on investment in health research.