Collaborative Research Centres are institutions established at universities and financed through the German Research Foundation (DFG) for a period of up to 12 years during which researchers pursue high-profile interdisciplinary research programmes.

There are currently three Collaborative Research Centers at the University of Oldenburg:

• Collaborative Research Centre 1372
  “Magnetoreception and navigation in vertebrates: from biophysics to brain and behaviour”
  University of Oldenburg, Institute of Avian Research/Wilhelmshaven, Max Planck Institute for Evolutionary Biology/Plön, Ruhr University Bochum, University of Cologne, Weizmann Institute of Science/Rehovot, Israel
  (Start 2019, Spokesperson: Prof. Dr. Henrik Mouritsen, University of Oldenburg)

• Collaborative Research Centre 1330
  „Hearing Acoustics: Perceptual Principles, Algorithms, and Applications (HAPPAA)“
  (Start 2018, Spokesperson: Prof. Dr. Volker Hohmann)
   
• Transregio 51
  „Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria“, University of Oldenburg, University of Braunschweig, Helmholtz Centre for Infection Research (HZI), Leibniz Institute DSMZ-German Collection for Microorganisms and Cell Cultures (DSMZ) and University of Göttingen with Göttingen Genomics Laboratory
  (Start 2010, Spokesperson: Prof. Dr. Meinhard Simon, University of Oldenburg)

• Transregio 31 "The active auditory system", Universities of Oldenburg and Magdeburg
  (2005 to 2017, Spokesperson: Prof. Dr. Georg Martin Klump, University of Oldenburg)

• Transregio 14 "Automatic Verification And Analysis of Complex Systems AVACS", Universities of Oldenburg, Freiburg and Saarbrücken
  (2004 to 2015, Spokesperson: Prof. Dr. Werner Damm, University of Oldenburg)