Further inquiries by the US authorities linked them to the radical Islamic militant group al-Qaeda which was set up by Osama Bin-Laden - the Saudi-born dissident who was already blamed by the US for attacking its embassies in East Africa and the warship USS Cole.
The US launched a military offensive in Afghanistan in an effort to track down Osama Bin Laden. It succeeded in shutting down the al-Qaeda training camps within the country and toppling the Taleban rulers of Afghanistan but has so far failed to find Bin Laden.
There is increasing frustration among American officials at their inability to find Bin Laden or some other senior al-Qaeda figures.
The US and its coalition allies have also vowed to eliminate the network of al-Qaeda cells thought to have been established throughout the Western world.
The US has sent dozens of al-Qaeda and Taleban suspects captured in Afghanistan and elsewhere to an American military base at Guantanamo Bay in Cuba.
International co-operation has led to hundreds of arrests in more than 50 countries, with several nations changing their laws to give them wider powers to apprehend alleged activists. In the US more than 1,100 people have been detained, many from Middle East countries, and charged with immigration offences.
Who is investigating?
The Federal Bureau of Investigation is at the centre of the investigation. Their results have not been disclosed.
Both the FBI and the Central Intelligency Agency have been criticised for failing to share and analyse information properly. Congress accused them of not "joining up the dots" before 11 September.
The Senate and House Intelligence oversight Committees are now investigating what went wrong.
Since the attacks, Attorney General John Ashcroft and FBI Director Robert Mueller have refocused the bureau's efforts on preventing future terrorist attacks. The powers of the FBI to detain people without charges have been widened in a move that has been criticised by human rights groups.
The attacks have led to a reassessment of how the FBI and the CIA operate and whether they are fulfilling their designated roles.
A Homeland Security department is being set up. It will control a number of government security and border agencies as well as co-ordinating operations between the FBI and CIA.
In addition, the FBI is organising a Washington-based 'super squad' of some 1,600 agents.
The ease with which people can now move across borders has involved a radical rethinking in intelligence sharing.
The CIA's Director George Tenet has assembled a group of more than a dozen countries to form an intelligence coalition. They are increasingly sharing sensitive intelligence on suspected terrorists and initiating arrests.
President Bush has said that his war on terrorism will not end until "every terrorist group of global reach has been found, stopped and defeated".
Intelligence agencies outside the US appear to have had some success in disrupting al-Qaeda since 11 September. Seven people were arrested in Morocco accused of planning attacks on British and US warships. Saudi authorities have also detained 13 people who were allegedly planning attacks within the kingdom, and there have been a string of arrests across Europe.
President Bush has used the state of war to justify the introduction of a raft of new legislation that widens his power and strengthens the hand of law enforcement.
In particular, he has called for the creation of military tribunals to try suspected terrorists who are not US citizens.
He has expanded the powers of the law enforcement agencies to fight terrorism, notably the USA Patriot Act, which expands the wire tapping powers of the FBI.
US officials have detained an undisclosed number of people without trial on immigration violations or on grounds that they maybe material witnesses in terrorism trials.
President Bush has also tightened the release of information on the investigation.
A federal order prevents officials from discussing detainees, and in most cases court files have been sealed and hearings are held behind closed doors.
Assessing the progress
So far only one person in the US - Zacarias Moussaoui - has been indicted for conspiring with Osama Bin Laden and others to attack the US on 11 September. He was detained shortly before the attacks.
Federal authorities say they have found no evidence indicating that any of the people arrested in the US since the attacks played a role in the hijacking plot.
But in Germany, a man has gone on trial in connection with the 11 September attacks.
Mounir al-Motassadek is charged with membership of a terrorist cell and of being an accessory to the murder of more than 3,000 people. He denies any knowledge of the attacks.
It looks like the international effort to track down accomplices is yielding more results than the domestic campaign.
Al-Qaeda members Mohammed Atef and Ali Qaed Senyan al-Harthi have both been killed by US forces. Other important suspects - Abu Zubaydah, Mohammed Zammar and Ramzi Binalshibh - have all been arrested.
Intelligence agents have reportedly foiled a number of planned attacks since 11 September, including a highly publicised plan to blow up the US Embassy in Paris.
The sheer number of arrests around the world - combined with other measures such as the freezing of bank accounts of suspected individuals and organisations - make it more difficult for al-Qaeda agents to operate.
But there are concerns about the methods some countries are using to obtain confessions, and the introduction of anti-terrorist legislation to detain suspects.
It may take many years before the full results of the investigation are released, and much of the detail that has been emerging is based on leaked reports and unattributed sources.
Civil libertarians have expressed outrage at anti-terror legislation passed in response to the attacks. Among their objections, they condemned the expanded use of secret surveillance and wiretaps previously restricted to foreign intelligence agents operating in the US.
Attorney General John Ashcroft vowed to use every legal means at his disposal against terrorism, promising to lock up suspects if they overstayed their visas by one day or broke local laws.
For the first time in 25 years, he rewrote investigative guidelines for the FBI, allowing the agency to monitor political or religious gatherings and the internet outside the course of an active investigation.
Civil libertarians said it eroded safeguards put in place in the wake of FBI excesses in the 1950s and 1960s.
Civil liberties groups have had some success in blocking attempts to detain indefinitely an undisclosed number of people under material witness provisions.
The Bush administration has also run up against some resistance in the courts in its efforts to keep secret the names of those detained on immigration charges.