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In 1999, the National Security Agency (NSA) launched the Center of Academic Excellence in Information Assurance Education (CAE-IAE) program. Under this program, an institution could receive the CAE-IAE designation if it passed rigorous curriculum and program requirements. By May 1999, seven schools became designated as a CAE, and soon, many more institutions joined the ranks of CAE-designated institutions. While the CAE-IAE program initially formed to address the shortage of intelligence community professionals, the program later expanded to address the lack of qualified cybersecurity professionals in the workforce.

In 2004, the Department of Homeland Security (DHS) became a co-sponsor of the CAE-IAE program. The program added a research designation (CAE-R) in 2008. In 2017, the CAE-IAE program name was changed to the CAE in Cyber Defense Education (CAE-CDE). A designation pathway for two-year colleges (CAE-2Y) began in 2019.

Today, the National Centers of Academic Excellence in Cybersecurity (CAE-C) program has over 300 institutions all over the Nation with designations in Cyber Defense Education, Research, and Cyber Operations.