Up the Khyber Pass in Landi Kotal, local militia opened fire to control about 5000 Pashtun tribesmen burning an effigy of President George W. Bush. Three protesters were injured.
In Karachi, pro-Taleban protesters blocked streets leading to the business centre and angry crowds burnt tyres and threw stones at vehicles.
Armoured vehicles with mounted machine guns were parked opposite the US consulate in Karachi. Police and paramilitary rangers guarded key installations.
Security was tightened at airports, ports, railway stations, power stations and government offices.
In the capital, Islamabad, United Nations staff were asked to stay at home, as 1000 student protesters, some armed with sticks or swords and chanting Islamic slogans, marched to the capital's American Center. Police in riot gear surrounded them.
"If helping poor Afghanistan is terrorism, then we are all terrorists," one student shouted.