Public funding for medical research in Germany is primarily provided by the German Research Foundation (DFG) and the Federal Ministry of Education and Research (BMBF). The aim of this study was to analyze the amount of national public funding for medical research on predominant causes of death in Germany, cardiovascular diseases and neoplasms, in relation to the burden of these diseases in Germany. Three evaluators categorized medical research projects funded by the DFG or BMBF between 2010 and 2012 into the categories "Diseases of the circulatory system" (with subgroups "Ischemic heart diseases", "Heart failure" and "Cerebrovascular diseases") and "Neoplasms". The total amount of public funding by the national agencies was analyzed in relation to the burden of disease for the respective disease condition. Information on national public funding for medical research of 2091million euros was available; of those, 246.8million euros (11.8%) were categorized being spent for research on "Neoplasms", 118.4million euros (5.7%) for research on "Diseases of the circulatory system". This results in 362.08 euros per case of death, 16.58 euros per year of life lost (YLL) and 16.04 euros per disability-adjusted life year (DALY) for "Neoplasms" and in 113.44 euros per case of death, 8.05 euros per YLL and 7.17 euros per DALY for "Diseases of the circulatory system". In Germany, research on cardiovascular diseases receives a lower share of national public funding for medical research compared to oncological research. These results are comparable to other European countries.