"We now face a spreading jihadist threat," she told the Senate Armed Services Committee. "We have driven a lot of the AQ [al-Qaida] operatives out of Afghanistan, Pakistan. We have killed a lot of them, including, of course, [Osama] bin Laden.
"But we have to recognize that this is a global movement," she said during testimony that largely focused on the Obama administration's handling of the Sept. 11, 2012, terrorist attack on the U.S. consulate in Benghazi, Libya.
Clinton said the French-led military intervention in Mali against armed Islamic insurgent groups was a crisis of great urgency.
"This is going to be a very serious, ongoing threat," Clinton said. "We are in for a struggle, but it is a necessary struggle. We cannot permit northern Mali to become a safe haven."
But she said al-Qaida's growing strength in the region threatened other allies, including oil-rich Nigeria, and the fledgling government in Libya.
She called al-Qaida "not only a terrorist syndicate [but also] a criminal enterprise" and said it still represented a threat to the United States, even though it has not attacked on U.S. soil since Sept. 11, 2001.
"What we have to do is to recognize we are in for a long-term struggle here," she told the senators. "That means we've got to pay attention to places that historically we have not chosen to or had to."
U.S. involvement has got to be more than simply anti-terrorist killings.
"We can kill leaders," she said, "but until we help establish strong democratic institutions ... we're going to be faced with this level of instability."
The instability is fueled by weapons from countries in the region, she said, citing particularly Libya after killed leader Moammar Gadhafi's well-stocked armories were looted.
"This Pandora's box of weapons coming out of these countries in the Middle East and North Africa is the source of one of our biggest threats," Clinton said.
"There's no doubt that the Algerian terrorists had weapons from Libya. There's no doubt that the Malian remnants of al-Qaida in the Islamic Maghreb have weapons from Libya. We have to do a much better job," she said.