The capture could be a significant blow to the Pakistani Taliban, who have waged a decade-long insurgency against Islamabad from sanctuaries along the Afghan border.
They have also helped the Afghan Taliban in their war against US-led NATO troops in Afghanistan.
Latif Mehsud was arrested by American forces as he was driving along a main highway in eastern Logar province's district of Mohammad Agha, said the Logar governor, Arsallah Jamal.
The road links the province with the Afghan capital, Kabul.
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The Pakistani Taliban confirmed the capture, but claimed Mehsud was seized by the Afghan army at the Ghulam Khan border crossing in the eastern province of Khost on Oct 5.
He was returning from a meeting to discuss swapping Afghan prisoners for money, said Pakistani Taliban commanders and intelligence officials, speaking on condition of anonymity because they were not authorized to talk to the media.
The Pakistani intelligence officials said American forces seized Mehsud while he was with the Afghan army, and that they no longer know where he is.