Background Universities undertake the majority of publicly funded research in Germany and hence bear a responsibility to contribute to global health efforts. So far, involvement and impact of German medical faculties in global health are unknown. Our aim was to systematically asses and evaluate German medical faculties’ contribution to global health related research and education, as well as their policies and practices concerning open access publishing and equitable licensing. Methods We assessed the involvement in global health of all 36 publicly funded medical faculties in Germany during 2010–2014 in three areas: innovation, access and education, using the following indicators: research funding and publications focused on global health or poverty-related and neglected diseases; open access publishing and policies promoting access to medical innovations worldwide; provision of global health education. Data were gathered from public databases, university websites and questionnaires sent to individual universities for validation and triangulation. Results There was a high level of variability between institutions and indicators. The proportion of research funding for poverty-related and neglected diseases research ranged between 0.0–1.1%. The top five institutions received nearly 85% of the total poverty-related and neglected diseases research funding. 20 of 36 universities had an institutional open access publishing policy, 19 had an open access publishing fund, 16 had neither. Only one university reported having used an equitable licensing policy. 22 of 36 faculties provided some global health education, but only one of them included global health in their core undergraduate medical curriculum as a compulsory course with more than just single lectures. Conclusion Obtained data indicate that global health and poverty-related and neglected diseases research at German medical faculties is highly concentrated in a few institutions, open-access publishing and equitable licensing policies are mostly absent, and only little global health education exists. Universities and government should address global health strategically in both research and education at medical faculties to reflect the country’s economic and political weight and human resource potential.