Rowley is well known for testifying as to concerns regarding the FBI ignoring information of a suspected terrorist during 9/11, which led to a two-year investigation by the Department of Justice.

Beginning in 1984, she spent six years working in the New York City field office on investigations involving Italian organized crime and Sicilian heroin.

After the September 11 attacks in 2001, Rowley wrote a paper for FBI Director Robert Mueller documenting how FBI HQ personnel in Washington, D.C., had mishandled and failed to take action on information provided by the Minneapolis, Minnesota, Field Office regarding its investigation of suspected terrorist Zacarias Moussaoui.

Moussaoui had been suspected of being involved in preparations for a suicide-hijacking similar to the December 1994 "Eiffel Tower" hijacking of Air France 8969.

(I know I shouldn't be flippant about this, but jokes were actually made that the key FBI HQ personnel had to be spies or moles like Robert Hanssen who were actually working for Osama Bin Laden to have so undercut Minneapolis's effort.

)[5][6][7]In May 2002 Rowley testified to the Senate and the 9/11 Commission about the FBI's pre-9/11 lapses due to its internal organization and mishandling of information related to the attacks.

Mueller and Senator Chuck Grassley (R-IA) pushed for and achieved a major reorganization, focused on creation of the new Office of Intelligence at the FBI.

[citation needed] In February 2003, Rowley wrote a second open letter to Mueller, in which she warned her superiors that the bureau would not "be able to stem the flood of terrorism that will likely head our way in the wake of an attack on Iraq".

[4] Rowley jointly held the Time magazine Person of the Year award in 2002 with two other women credited as whistleblowers: Sherron Watkins from Enron and Cynthia Cooper of WorldCom.

Rowley had formerly voted and identified as a Republican, but on June 27, 2005, she announced that she was entering the race as a DFLer, and on July 6 officially kicked off her campaign at her home.

[6] Rowley authored a chapter in Patriotism, Democracy, and Common Sense: Restoring America's Promise at Home and Abroad.