Brookhaven National Laboratory (BNL) is a multipurpose research laboratory housing large, state-of-the-art facilities such as RHIC, NSLS-II, and the Center for Functional Nanomaterials. Stony Brook is a partner in Brookhaven Science Associates LLC, managing the Laboratory for the Department of Energy. Located less than 20 miles from campus, Brookhaven provides many opportunities for collaborative research efforts.

Brookhaven Science Associates (BSA) was established for the sole purpose of managing and operating Brookhaven National Laboratory. Formed as a partnership between Battelle Memorial Institute and The Research Foundation of State University of New York (SUNY) on behalf of Stony Brook University (SBU), BSA is the legal entity responsible for leading BNL successfully through the 21st century.

Both SBU and Battelle are strongly motivated to ensure Brookhaven's continuing success. Being Brookhaven's closest university neighbor, Stony Brook is the single largest user of BNL facilities; BNL facilities and its scientific staff are essential to the vitality of the university's intellectual life and to the impact of many of its research programs. BNL and the Univesrity share an increasing number of joint faculty appointments.

The Office of Brookhaven National Laboratory Affairs coordinates all activities between Stony Brook and Brookhaven. Its mission is to continually enhance the relationship between the two institutions by developing and supporting initiatives that bring faculty, students and staff together in scientific, educational, and cultural activities.