The Federal Ministry of Education and Research has two offices, one in Bonn, the other in Berlin. The basis for this division between the "old" seat of government and the capital is the Bonn/Berlin Act which is intended to offset the consequences for the Bonn region resulting from the move to Berlin by parliament and government. One of the key aims is to expand Bonn as a centre for scientific and research activities.

The Federal Ministry of Education and Research is located on the city boundary between Bonn and Bad Godesberg. It was built in 1974, together, at the time, with the Federal Ministry of Justice. The complex in the Heinemannstraße comprises two cross-shaped buildings, 11 and 14 storeys high respectively, a few smaller office buildings and a canteen. The 14-storey building has a basement which houses the library, cafeteria, conference rooms and a printing shop. The majority of the roughly 1,000 members of staff at the BMBF work in these so-called "Kreuzbauten". The site's expansive gardens form an ideal setting for works of art from the 70s and 80s.
The Bonn premises lie in the centre of the new scientific district which is developing in the city. This proximity facilitates cooperation. Central establishments include: Stiftung caesar (Center of Advanced European Studies and Research), which is setting up a research centre focussing on future-oriented technologies in the natural and engineering sciences, the Fachhochschule Bonn-Rhein-Sieg (University of Applied Sciences), the centres for Europäische Integrations- (ZEI) (European Integration) and Entwicklungsforschung (ZEF) (European Development Research) of the University of Bonn, and the extended Wissenschaftszentrum (Scientific Centre) Bonn. Further important research and educational establishments in Bonn are: the Bundesinstitut für Berufsbildung (Federal Institute for Vocational Training), the offices of the Bund-Länder-Kommission für Bildungsplanung (Commission for Educational Planning) and the Secretariat of the Kultusministerkonferenz (Conference of Ministers of Education and Cultural Affairs).

German history was written at the site of the offices of the BMBF in the Hannoversche Straße in Berlin. The original building was constructed as a barracks between 1912 and 1914. The Berlin-Mitte Police School moved into the building in 1938. After World War II, the premises were handed over to the Academy of Arts and Sciences for rebuilding and further use. The architect Hans Scharoun extended the attic to make a studio in 1949. A year later, the building was transferred to the German Building Academy. It was here that the architect Hans Henselmann and his colleagues planned the redevelopment of central East Berlin and the rebuilding of the eastern parts of the city.
In 1973/74, the building was revamped and became the seat of the Permanent Mission of the Federal Republic of Germany to the GDR. For conferences, an adjoining building was added in 1975. The Mission became a focus of the new German "Ost-Politik" which eased the consequences of the division of Germany for people on both sides of the border with its "policy of small steps". In 1984 and again in the historic weeks of transition in 1989, many citizens of the GDR who sought to leave their country found refuge in the Permanent Mission and waited for their exit papers there. The Permanent Mission completed its work on the day of German reunification. The building, which is now protected by a conservation order, was taken over by the BMBF. The Minister and her staff moved into their new offices in 1999.
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