The terrorist attacks of September 11, 2001, and the subsequent anthrax mail attacks, have had a profound impact on Americans’ personal and professional lives and have sparked an active debate regarding the delicate balance between the need for national security and the pursuit of academic freedom. Although academic freedom can be defined in many ways, there are four primary tenets of freedom in an academic environment: freedom to research, freedom to publish, freedom to teach, and freedom to speak. Each of these tenets has come under attack in the wake of September 11, 2001. In this report the author further defines academic freedom and reflects upon recent events that have had a real or perceived impact on this freedom, including (1) attempts to categorize and restrict some research as “sensitive,” (2) implementation of export control laws and select agent regulations, (3) limitations on the publication of research findings, (4) prohibition of certain foreign nationals from collaborating with U.S. researchers and receiving education and training in U.S. colleges and universities, and (5) restraint of faculty free speech. The author offers some suggestions as to how academia might achieve a proper balance between protecting our national security while promoting and maintaining academic freedom.