Petraeus had been in charge of the 140,000 international NATO forces for the past year, overseeing the surge of U.S. troops by another 30,000 last year to target the overwhelming Taliban insurgency.
Gen. Allen takes over command as NATO forces are beginning to withdraw and hand over responsibility for security to Afghan forces. Allen previously headed U.S. Central Command.
Allen said he wants Afghanistan to be free of the extremism and terrorism that has troubled the country for years and hopes to see Afghanistan grow more stable and secure, reports VOA.
Allen said there will be "tough days ahead" but that he intends to keep up the "momentum of the campaign."
There has been a series of high-level assasinations of key Afghan figures in the last week including Afghan President Hamid Karzai’s half brother Ahmad Wali Karzai, head of the Kandahar provincial council, and Jan Mohammed Khan a key adviser to the president.
In a release by NATO, Secretary-General Anders Fogh Rasmusssen thanked Petraeus for the "tremendous contribution he has made to our mission in Afghanistan." He also thanked him for the work he did preparing for Afghan security forces to take over.
On Sunday, Afghan forces began the transfer process with the handover of the central Bamiyan area to Afghan forces. A ceremony Sunday marked the handoff of responsibility from New Zealand troops to local forces.
Petraeus will return to the United States to head the CIA.
