Comey was born in Yonkers, New York, where his parents, Joan Marie Comey (nee Herald) and J. Brien Comey, lived. His grandfather, William J. Comey, was an officer and later commissioner of the Yonkers Police Department. The family moved to Allendale, New Jersey, in the early 1970s. His father worked in corporate real estate and his mother was a computer consultant and homemaker.

In early January 2006, The New York Times, as part of its investigation into domestic surveillance by the National Security Agency, reported that Comey, who was Acting Attorney General during the March 2004 hospitalization of John Ashcroft, refused to certify the legality of central aspects of the NSA program. The certification was required under White House procedures in order for the program to continue.  In March 2004, Federal Bureau of Investigation Director Robert S. Mueller III and Comey threatened the Bush administration with their resignations if the White House overruled the DOJ finding that the domestic wiretapping under the Terrorist Surveillance Program (TSP) was unconstitutional, if such were done without a court warrant. On March 10, 2004, United States Attorney General (USAG) John Ashcroft was being visited by his wife as he was treated in the intensive care unit at the George Washington University Hospital. She solicited Mueller and Comey to join them, and shortly after their arrival, they were joined by Jack Goldsmith of the DOJ's Office of Legal Counsel and Patrick Philbrin. In Goldsmith's 2007 memoir, he said Comey had come to the hospital to give Ashcroft support in withstanding pressure from the White House. None of the four visitors wanted the TSP reauthorized. After the quartet's arrival, Ashcroft refused to give his consent to its extension, despite being pressured at the hospital soon afterward by Andrew H. Card Jr., White House Chief of Staff, and Alberto R. Gonzales, then-White House counsel and future Attorney General. The two were requesting that Ashcroft waive the DOJ ruling and permit the domestic warrantless eavesdropping program to continue beyond its imminent expiration date. Ashcroft additionally informed the pair that due to his illness, he had delegated his powers as USAG to Comey. Comey later confirmed these events took place (but declined to confirm the specific program) in testimony to the United States Senate Judiciary Committee on May 16, 2007. FBI director Mueller's notes on the March 10, 2004, incident, which were released to a House Judiciary committee, confirms that he "Saw (the) AG, John Ashcroft in the room (who was) feeble, barely articulate, clearly stressed."  Comey and Mueller withdrew their threats to resign after meeting directly on March 12, 2004, with President Bush, who gave his support to making requisite changes in the surveillance program.

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United States Attorney General (USAG) John Ashcroft was being visited by his wife as he was treated in the intensive care