The September 11 attacks were carried out by 19 hijackers of the Islamist militant organization al-Qaeda. In the 1990s, al-Qaeda leader Osama bin Laden declared a militant jihad against the United States, and issued two fatawa in 1996 and 1998. In the 1996 fatawa, he quoted the Sword Verse. In both of these fatawa, Bin Laden sharply criticized the financial contributions of the American government to the Saudi royal family as well as American military intervention in the Arab world.

These motivations were published in Bin Laden's November 2002 Letter to the American people, in which he said that al-Qaeda's motives for the attacks included Western support for attacking Muslims in Somalia, supporting Russian atrocities against Muslims in Chechnya, supporting the Indian oppression against Muslims in Kashmir, condoning the 1982 massacres in Lebanon, the presence of US troops in Saudi Arabia, US support of Israel, and sanctions against Iraq. Bin Laden and Ayman al-Zawahiri asserted that Israeli repression of Palestinians during the Second Intifada was the immediate cause that forced Al-Qaeda to launch the September 11 attacks.

Following the attacks, the Bush administration asserted that al-Qaeda attacked the United States because "they hate us for our freedoms". George W. Bush said in a speech to Congress nine days after the attacks that "They hate what we see right here in this chamber — a democratically elected government. Their leaders are self-appointed. They hate our freedoms — our freedom of religion, our freedom of speech, our freedom to vote and assemble and disagree with each other." Al-Qaeda leadership maintained that United States was targeted in retaliation for its imperialist aggression against the Muslim world. In a speech released in 2004, Osama Bin Laden stated: "free men do not forfeit their security, contrary to Bush’s claim that we hate freedom. If so, then let him explain to us why we don’t strike for example – Sweden?"

Before the attacks, Al-Qaeda issued proclamations that provide insight into the motivations for the attacks: one was the fatwā of August 1996, and a second was a shorter fatwā in February 1998. Both documents appeared initially in the Arabic-language London newspaper Al-Quds Al-Arabi. Bin Laden's 1998 fatwā stated:

"The ruling to kill the Americans and their allies -- civilians and military -- is an individual duty for every Muslim who can do it in any country in which it is possible to do it, in order to liberate the al-Aqsa Mosque and the holy mosque [Mecca] from their grip, and in order for their armies to move out of all the lands of Islam, defeated and unable to threaten any Muslim. This is in accordance with the words of Almighty God, "and fight the pagans all together as they fight you all together," and "fight them until there is no more tumult or oppression, and there prevail justice and faith in God.""

The fatwā also denounced the presence of US troops in Saudi Arabia and asserted that Americans were attempting to balkanize and destabilize the Arab world with the intent of guaranteeing "Israel's survival":

"..for over seven years the United States has been occupying the lands of Islam in the holiest of places, the Arabian Peninsula, plundering its riches, dictating to its rulers, humiliating its people, terrorizing its neighbors, and turning its bases in the Peninsula into a spearhead through which to fight the neighboring Muslim peoples."

After the attacks, bin Laden and Ayman al-Zawahiri published dozens of video tapes and audio tapes, many describing the motivations for the attacks. Two particularly important publications were bin Laden's 2002 Letter to the American people, and a 2004 video tape by bin Laden. In addition to direct pronouncements by bin Laden and Al-Qaeda, numerous political analysts have postulated motivations for the attacks.