OBJECTIVES: The concept of allocation of research funding in health care depending on the disease-specific burden to the society was proposed by the governmental institutions in the USA and Europe. Unfortunately, recent data from the USA showed that this concept has been unsuccessfully implemented. The objective was to perform a systematic review of allocation of research funding in health care in Europe. METHODS: We performed a systematic review of all publications, which investigated the allocation of research funding in health care of different European countries in the last 10 years (234 hits). In Germany, we interviewed the main state funding institutions to acquire data on allocation of funding in national health care. Data on funding allocation were compared with disability-adjusted life years (DALY), prevalence and costs of diseases. RESULTS: Data on funding allocation are not available for the most European countries. Disease burden was inadequately reflected in those countries where data were available. A comparison between cancer, coronary heart disease, dementia and stroke, which are among the most common causes of mortality and disability in Europe, revealed that cancer receives over 70% of total research funding. Although the health-economic burden of dementia and cancer is similar, dementia receives approximately 10 times less funding. In the UK, Switzerland and Denmark, cancer receives 49.175€, 25.162€ and 24.424€ of funding per one million of costs. The research funding per one million of costs is substantially lower in dementia (2.145€ in UK, 11.300€ in Switzerland und 6.808€ in Denmark), and stroke (4.693€, 15.000€ and 11.788€, respectively). CONCLUSIONS: Disease burden is still inadequately reflected in allocation of research funding in Europe. There is an underfunding of research in brain diseases, such as stroke and dementia, which are associated with substantial economic burden. Health-political solutions are necessary to improve the implementation of the research funding concept.