Pipes' think tank the Middle East Forum established a website in 2002 called Campus Watch, which identified what it saw as five problems in the teaching of Middle Eastern studies at American universities: "analytical failures, the mixing of politics with scholarship, intolerance of alternative views, apologetics, and the abuse of power over students." According to The New York Times, Campus Watch is the project for which Pipes is "perhaps best known."

Through Campus Watch, Pipes encouraged students and faculty to submit information on "Middle East-related scholarship, lectures, classes, demonstrations, and other activities relevant to Campus Watch". The project was accused of "McCarthyesque intimidation" of professors who criticized Israel when it published "dossiers" on eight professors it thought "hostile" to America. In protest, more than 100 academics demanded to be added to what some called a "blacklist". In October 2002 Campus Watch removed the dossiers from its website.