The facility is located on the EMBL campus and used by both EMBL and DKFZ scientists to find and validate molecules both for drug precursors and for basic research.
Dr Iain Mattaj, EMBL scientific director, said: "Within academic research, this is an emerging area - very few of these facilities exist in Europe."
"Our researchers wanted such services as a tool for system biology research - to understand the big picture of biology, rather than looking at the individual pieces. This facility will give our researchers access to very valuable resources to do this."
Six full-time employees at the facility will be working to serve the needs of both organisations providing services that include screening hit validation and developing assays on a high throughput scale.
Dr Michael Pawlita, project leader at the DKFZ, added:"Scientists at the DKFZ needed a way to find small molecules that can serve as effective drugs against cancer. We can use the compound library to find molecules that could lead to effective drugs."
The EMBL was established in 1974 and is supported by 17 countries including nearly all of Western Europe and Israel. Its outstations provide European biologists access to large instruments for the study of protein structures, some of the world's oldest and biggest databases of DNA and protein sequences.