The film covers anti-military protests at UC Santa Cruz and San Francisco State University, treatment of conservative students at Cal Poly and the University of Tennessee, racial and ethnic politics at the University of Michigan and Yale, teaching at Duke and Columbia, among other subjects. It also includes interviews with David French and Greg Lukianoff, (then respectively president and director of legal and public advocacy at the Foundation for Individual Rights in Education), Glenn Reynolds, Daniel Pipes and others.
Maloney spent two and a half years making the documentary by conducting interviews on various college campuses and with various thinkers. The film was preceded by two shorter versions, Brainwashing 101 and Brainwashing 201: The Second Semester. The two shorts led the 2004 American Film Renaissance festival to select Indoctrinate U as its "most anticipated documentary."
In March 2007, Maloney appeared on Hannity's America to discuss the film. On April 19 of the same year, he appeared on C-SPAN's Washington Journal where they showed clips from the film and took calls.
Indoctrinate U was produced by On the Fence Films with the support of the Moving Picture Institute, and Stuart Browning, Blaine Greenberg, and Thor Halvorssen. The film's executive producers are Stuart Browning and Blaine Greenberg. Its associate producer is Frayda Levy. It was edited by Chandler Tuttle.
Examples of "intellectual thuggery" in the film is nothing more than "the tip of a disgusting iceberg", laments Walter E. Williams, noting that "Several university officials refused to be interviewed for the documentary. They wanted to keep their campus policies under wraps, not only from reporters but parents as well.
On November 13, 2007, the official website was taken down and replaced with a notice that read: "Due to threatened legal action from a major taxpayer-funded university, we've temporarily taken down the Indoctrinate U homepage while we assess our options." The website was back up by December 4. Maloney explained in a statement that Indiana University claimed there was a similarity between the university's logo and that of the film's. The Indoctrinate U logo was changed and the website resumed operation.