Issues related to terrorism and violent insurgencies are at the forefront of U.S. and international security policy. CISAC researchers are engaged in scholarship dedicated to exploring the nature and organizational structure of international terrorist organizations, and how best to prevent, mitigate, or counter violence committed by non-state actors. This area of research focuses in particular on the legal, historical, political, technical and organizational issues related to the development and evaluation of effective counter-terrorism and counterinsurgency strategies, both in the U.S. and abroad.

Projects in this research area include Martha Crenshaw's multi-year examination of the roots of violent extremist groups that maps the evolution of terrorist organizations. Senior research scholar Joseph Felter, working alongside former CISAC fellow Jacob Shapiro, co-directs the Empirical Studies of Conflict program, which collects, disseminates, and analyzes conflict data from a variety of nations including Iraq, Afghanistan, and Colombia in an effort to better understand conflicts and insurgencies. Active-duty U.S. military officers spend time in residence at CISAC each year conducting research on strategies for effective counter-insurgency and counter-terrorist operations, among other issues.

Other researchers, including Charles Perrow and Lawrence Wein, have published papers and books on the organization of homeland security, border and port security preparedness, and strategies for managing the aftermath of a catastrophic terrorist event. Paul Stockton's work has focused on how U.S. security institutions respond to changes in threats, including the rise of terrorism, and the interaction of U.S. Congress and the executive branch in restructuring national security budgets, policies, and institutional arrangements. Michael May and William Perry have also done significant work on managing the threat of nuclear terrorism.