In the light of big data driven clinical research, fair access to real world clinical health data enables evidence to improve patient care. Germany’s healthcare system provides an abundant data resource but unique challenges due to its federated nature, heterogeneity and high data-protection standards. The Medical Informatics Initiative (MII) developed concepts that are being implemented in the German Portal for Medical Research Data (FDPG) to grant access to distributed data-sources across state borders. The portal currently provides access to more than 10 million patient resources containing hundreds of millions of laboratory parameters, diagnostic reports, administered medications, procedures and specimens. Upcoming datasets include among others oncological data, molecular analysis results and microbiological findings. Here, we describe the philosophy, implementation and experience behind the framework: standardized access processes, interoperable fair data, software for in depth feasibility requests, tools to support researchers and hospital stakeholders alike as well as transparency measures to provide data use information for patients. Challenges remain to improve data quality and automatization of technical and organizational processes.