Aid workers and diplomats have left Kabul
Afghans fear they will be made to pay the price for the fact that their leaders, the Taleban, are hiding Saudi dissident Osama Bin Laden, the man the US suspects masterminded the attacks.
Muslim militants, known as Afghan Arabs, have fled the capital city of Kabul. residents say, and others have started digging trenches around the city.
And amid the fears of a US operation, diplomats representing eight foreign aid workers on trial for spreading Christianity have also left the city for Pakistan.
'School for terrorists'
The US has previously described Afghanistan as a "school for terrorists". Muslim militants from the Middle East, Philippines, Central Asia and China have trained there.
Militants are now reported to have evacuated their bases around the country.
Now there are rumours the Taleban have put Mr Bin Laden under house arrest.
The BBC's correspondent in Afghanistan, Kate Clark, said the Taleban might just be saying this to appease the West, and perhaps avert a retaliatory strike.
And the BBC's John Simpson said a source who had met Mr Bin Laden just two days ago said the Saudi dissident had been stripped of all of his complicated and sophisticated communications equipment.
An aide for Mr Bin Laden quoted him as denying he had planned the attack, but calling it a "punishment from Allah".
"I have no information about the attackers or their aims and I don't have any links with them," the aide quoted Mr Bin Laden as saying.
Despite growing fears of what Afghans see as an inevitable US attack, Kabul remains largely calm, with markets and bazaars bustling as usual.
Pakistan will cooperate
In the meantime, Pakistan has said it would cooperate with the United States.
"All countries must join hands in this common cause," said Pakistan's military ruler General Pervez Musharraf on national television.
"I wish to assure President Bush and the US government of our fullest cooperation in the fight against terrorism," he said.
In 1998, Pakistan refused to allow US aircraft permission to fly over its airspace for a retaliatory operation against Mr Bin Laden, who was blamed for two deadly bomb attacks on US embassies in Kenya and Tanzania.
Foreigners leave
Most foreigners, mainly aid workers, left the country on Wednesday amid fears of a US strike.
"We hope that the Taleban government will take care of their personal safety and security," German diplomat Helmut Landes told Reuters.
Their relatives are also leaving and Deborah Oddy, the mother of one of the detainees, Heather Mercer, wept as she left Kabul.
Trial
The United Nations is temporarily shutting down its operations in Afghanistan which means that there will be no more flights out of the country after Thursday.
It also leaves the arrested aid workers with little support.
Two Americans, two Australians and six Germans are being held in detention in Kabul, charged with spreading Christianity. If found guilty they could face the death penalty.
The diplomats are leaving them in the hands of a Pakistani Islamic scholar, who will act as their legal counsel.
They are being tried by Islamic judges, in the Taleban supreme court.
The eight detainees will be the only foreigners left in Afghanistan, apart from journalists and a few key staff from the International Red Cross and Medicins Sans Frontiere.