- Center for Algorithms & Interactive Scientific Software (CAISS)
- Center for Analysis of Structures and Interfaces (CASI)
- Center for Information Networking and Telecommunications (CINT)
- Center for Mesoscopic Modeling and Simulation
- Center for Metamaterials (CfM)
- Center for Water Resources and Environmental Research (CWRER)
- CUNY Center for Advanced Technology (CAT)
- CUNY Energy Institute
- CUNY Institute for Municipal Waste Research
- CUNY Institute for Transportation Systems (ITS)
- CUNY Institute for Urban Systems (CIUS)
- Environmental Science and Engineering Institute (ESEI)
- Institute for Ultrafast Spectroscopy and Lasers (IUSL)
- International Center for Environmental Resources and Development
- Benjamin Levich Institute for Physico-Chemical Hydrodynamics
- National Oceanic and Atmospheric Administration / Cooperative Remote Sensing Science and Technology (NOAA-CREST)
- New York Center for Biomedical Engineering (NYCBE)
- New York State Center for Advanced Technology in Ultrafast Photonics
- University Transportation Research Center (UTRC)
Two of these research centers, IUSL and CASI, are housed in the Science Division, and GSOE faculty participate in their administration and research activities.
The CCNY Office of Research Administration encourages, develops budgets for and administers most regulatory aspects of research grants and contracts. It provides a local interface to the Research Foundation of CUNY, the fiscal custodian of all CUNY research grants.