A $25m reward was offered for Sheikh Mohammed's capture
The interrogation of the suspected planner of the 11 September 2001 attacks, Khalid Sheikh Mohammed, is said to have begun.
The 37-year-old Kuwaiti was arrested with two other people in a joint Pakistani-CIA operation near the Pakistani capital of Islamabad on Saturday.
His current whereabouts remain unknown, but correspondents say US authorities will want to hold him in a remote and secure location such as their base in Bagram in Afghanistan or on a warship offshore.
Washington has described him as one of al-Qaeda leader Osama Bin Laden's "most senior and significant lieutenants".
His capture prompted joy in the US Government.
"That's fantastic!" was President George W Bush's reported reaction to the news.
Khalid Sheikh Mohammed had long been on the FBI's most wanted list, and the US had recently increased the reward for his capture to $25m.
The whereabouts of Bin Laden remain unknown
On Sunday his picture on the website showed a red strip over the front marking that he had been located
BBC correspondent Nick Childs says that Bush administration has been under pressure at home from critics who complain it has neglected the hunt for al-Qaeda as it focussed on Iraq, and the arrests will take some of that heat off.
He has been indicted in America for plotting to blow up American commercial airliners in the Philippines in the mid-1990s.
Rashid Qureshi, a spokesman for Pakistan's President Pervez Musharraf described the Kuwaiti as "the kingpin of al-Qaeda".
Hunt for al-Qaeda
US intelligence agents have been hunting remnants of Afghanistan's former Taleban regime and Osama Bin Laden's al-Qaeda network since the US-led military action in Afghanistan in late 2001.
Hundreds al-Qaeda militants and former Taleban ministers are thought to have fled into Pakistan since US-led forces launched the strikes following the 11 September attacks.
Dozens have subsequently been arrested, including senior al-Qaeda leader Ramzi Binalshibh, a Yemeni national.
He is alleged to have been one of the main planners of the attacks in Washington and New York. He is also in US custody.
Pakistan has been hunting al-Qaeda and Taleban remnants
Another top al-Qaeda suspect, Abu Zabaydah, thought to have been Bin Laden's field commander, was captured in March 2002.
He was subsequently handed over to the US and is said to have been co-operating with investigators.
He is also thought to have been the source behind many of America's terror warnings since the 11 September attacks.
Bin Laden whereabouts
Right-wingers in the Pakistani Government have strongly opposed any US intervention in raids or searches for al-Qaeda suspects.
BBC Islamabad correspondent Paul Anderson says that Sheikh Mohammed's capture strikes at the heart of the al-Qaeda network.
And, he says, it is bound to raise speculation as to the whereabouts of Osama Bin Laden, whom some experts believe may be hiding in the Afghan-Pakistan border area.