In a statement, David Petraeus said he had submitted his resignation to President Barack Obama, and that he had shown “extremely poor judgement”.
He described his behavior as “unacceptable” for the leader of the nation’s main intelligence agency.
David Petraeus became CIA boss in 2011 after heading international forces in Iraq, then in Afghanistan.
He was the highest-profile military officer of the post-9/11 years, winning plaudits for his role running the “surge” in Iraq and implementing a counter-insurgency strategy in Afghanistan.
David Petraeus’ resignation came just three days after President Barack Obama’s re-election, and prompted a flurry of statements from the White House, intelligence community and General Petraeus himself.
Announcing his decision to stand down, the former general was full of contrition.
“After being married for over 37 years, I showed extremely poor judgment by engaging in an extra-marital affair,” David Petraeus said in a statement.
“Such behavior is unacceptable, both as a husband and as the leader of an organization such as ours. This afternoon, the president graciously accepted my resignation.”
Barack Obama’s statement said Mr Petraeus had “provided extraordinary service to the United States for decades”, citing both his time as CIA director and service to the military.
“By any measure, through his lifetime of service David Petraeus has made our country safer and stronger.”
“Going forward, my thoughts and prayers are with Dave and Holly Petraeus, who has done so much to help military families through her own work.”
CIA deputy director Michael Morell will serve as acting director of the agency, the White House confirmed.
James Clapper, director of national intelligence, thanked David Petraeus for his decades of service: “Dave’s decision to step down represents the loss of one of our nation’s most respected public servants.
“I have spent more than five decades serving our country-in uniform and out-and of all the exceptional men and women I have worked with over the years, I can honestly say that Dave Petraeus stands out as one of our nation’s great patriots.”
David Petraeus is believed to have feared that his infidelity would eventually become public, and therefore took the decision to quit before he was forced out.
Extra-marital affairs are considered particularly damaging for intelligence officials due to the confidential nature of their work and the risk they could leak national security secrets.
David Petraeus, 60, has been married to Holly, née Knowlton, since 1975, after they meet when he was a military cadet at West Point and she was the daughter of the academy’s superintendent.
When he was sworn in as director of the CIA by Vice President Joe Biden, Holly held the Bible on which he swore his oath of office.
David Howell Petraeus is a retired U.S. Army four-star general and the most celebrated American soldier of his time.
Known as a scholar and a warrior, the West Point graduate is admired as much for his intellect as his tactical ability and charisma on the battlefield.
He oversaw the crafting of the successful 2006 U.S. counterinsurgency measures in Iraq and accepted without hesitation Barack Obama’s request to leave Central Command in 2010 and lend his expertise to the failing international effort in Afghanistan.
Spending 37 years in the military, David Petraeus retired from service and took up his post as director of the CIA on September 6, 2011.
Born in Cornwall-on-Hudson in New York in 1952, David Petraeus is the son of small town librarian Miriam and Sixtus, a sea captain who had emigrated from the Netherlands.
Immediately upon his graduation from high school in 1970 he enrolled as a cadet at West Point Military Academy where he served with distinction – graduating in the top five of his class in 1974.
Just after his graduation he married Holly Knowlton, daughter of West Point superintendent General William A. Knowlton.
Despite his close working relationship with Barack Obama and other Democratic officials, David Petraeus was spoken of as a possible running mate for Republican presidential candidate Mitt Romney this year.
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