[5] Mukasey, pursuant to the Foreign Agents Registration Act (FARA), is registered as working on behalf of the National Council of Resistance of Iran.

[21] During his service on the bench, Mukasey presided over the criminal prosecution of Omar Abdel Rahman and El Sayyid Nosair, whom he sentenced to life in prison for a plot to blow up the United Nations and other Manhattan landmarks uncovered during an investigation into the 1993 World Trade Center bombing.

"[23] Mukasey also presided over the trial of Jose Padilla, ruling that the U.S. citizen and alleged terrorist could be held as an enemy combatant but was entitled to see his lawyers.

[24] On October 14, 2004, citing U.S. Supreme Court precedent, Mukasey reversed his September 2002 decision and dismissed a case in which plaintiffs in twenty consolidated actions sued the Italian insurance company Generali S.p.A. (Generali), seeking damages for nonpayment of insurance proceeds to beneficiaries of policies purchased by Holocaust victims before the end of World War II.

[25] In so ruling, Mukasey gave deference to "a federal executive branch policy favoring voluntary resolution of Holocaust-era insurance claims.

[27] On the March 18, 2007, episode of Meet the Press, Senator Chuck Schumer suggested Mukasey as a potential Attorney General nominee who, "by [his] reputation and career, shows that [he] put rule of law first.

[31] In May 2004, while still a member of the judiciary, Mukasey delivered a speech (which he converted into a The Wall Street Journal opinion piece) that defended the USA PATRIOT Act; the piece also expressed doubt that the FBI engaged in racial profiling of Arabs and criticized the American Library Association for condemning the Patriot Act but not taking a position on librarians imprisoned in Cuba.

[31] On August 22, 2007, The Wall Street Journal published another op-ed by Mukasey, prompted by the resolution of the Padilla prosecution, in which he argued that "current institutions and statutes are not well suited to even the limited task of supplementing a military effort to combat Islamic terrorism."

Mukasey instead advocated for Congress, which "has the constitutional authority to establish additional inferior courts," to "turn [its] considerable talents to deliberating how to fix a strained and mismatched legal system.

Mukasey refused to state a clear legal position on the interrogation technique known as waterboarding (in which water is poured over a rag on the prisoner's face to simulate drowning).

Leahy and the other nine Democratic committee members indicated to Mukasey, via letter, that they were "deeply troubled by your refusal to state unequivocally that waterboarding is illegal during your confirmation hearing..."[37] It appeared that Mukasey may have been concerned about the potential pursuit of government employees or agents, and their authorizing superiors, in American or foreign courts under criminal charges, when responding to the Senate Judiciary committee questions.

[38][39] In describing the issue's challenges to the Bush administration, The New York Times quoted Scott L. Silliman, director of the Center on Law, Ethics and National Security at Duke University, as saying about such court cases, which could ultimately reach the president: "You would ask not just who carried it out, but who specifically approved it."

It was believed that secret Justice Department legal opinions approved waterboarding and other procedures officially called "harsh interrogation techniques".

[50] Newspaper reports assumed that Mukasey would further recuse himself from cases involving Bernard Kerik, a former New York City police commissioner under Giuliani, who was under federal investigation for bribery and other offenses.

[53] During an Oval Office meeting with Rudy Giuliani in 2017, Mukasey pressed Secretary of State Rex Tillerson for the release of the indicted Turkish-Iranian gold trader, Reza Zarrab.

[55][56] Speaking in London on March 14, 2008, Mukasey said that he hopes the detainees currently charged with participating in the September 11 attacks are not executed if found guilty in order to avoid creating any martyrs.

[65] Asked directly if Mukasey was a liar because he claimed that enhanced interrogation produced useful intelligence, Senator John McCain stated unequivocally, "Yes, I know that he is.

"[66] On April 18, 2018, Mukasey published an op-ed piece in The Wall Street Journal entitled "Trump, Cohen and Attorney-Client Privilege" attacking the use of a search warrant by the federal government to search Cohen's legal records, and attacking the track records of former FBI directors/assistant US Attorneys Robert Mueller and James Comey.