The aircraft hijackers in the September 11 attacks were 19 men affiliated with al-Qaeda, a jihadist organization based in the Islamic Emirate of Afghanistan. They hailed from four countries: 15 of them were citizens of Saudi Arabia, two were from the United Arab Emirates, one was from Egypt, and one from Lebanon. To carry the attacks out, the hijackers were organized into four teams, each led by a pilot-trained hijacker who would commandeer the flight with three or four "muscle hijackers" who were trained to help subdue the pilots, passengers, and crew. Each team was assigned to a different flight and given a unique target to crash their respective planes into. Mohamed Atta was the assigned ringleader over all four groups.

The first hijackers to arrive in the United States were Khalid al-Mihdhar and Nawaf al-Hazmi, who settled in San Diego County, California, in January 2000. They were followed by three hijacker-pilots, Hamburg cell members Mohamed Atta, Marwan al-Shehhi, and Ziad Jarrah in mid-2000 to undertake flight training at Huffman Aviation flight-training school in Venice, Florida. The fourth hijacker-pilot, Hani Hanjour, who was not a member of the Hamburg cell, arrived in San Diego in December 2000. The rest of the "muscle hijackers" arrived in early- and mid-2001.

Khalid al-Mihdhar and Nawaf al-Hazmi were both experienced and respected jihadists in the eyes of al-Qaeda's leader Osama bin Laden.

As for the pilots who would go on to participate in the attacks, three of them were original members of the Hamburg cell (Mohamed Atta, Marwan al-Shehhi, and Ziad Jarrah). Following their training at al-Qaeda training camps in Afghanistan, they were chosen by bin Laden and al-Qaeda's military wing due to their extensive knowledge of Western culture and language skills, increasing the mission's operational security and its chances for success. Mohamed Atta himself was immediately given command over the planning and execution of the attack upon his arrival in Afghanistan in January 2000. The fourth intended pilot, Ramzi bin al-Shibh, a member of the Hamburg cell, was also chosen to participate in the attacks, but he was unable to obtain a visa for entry into the United States. He was later replaced by Hani Hanjour, a Saudi national.

Al-Mihdhar and al-Hazmi were also potential pilot hijackers but did not do well in their initial pilot lessons in San Diego. Both were kept on as "muscle" hijackers, who would help overpower the passengers and crew and allow the pilot hijackers to take control of the flights. In addition to al-Mihdhar and al-Hazmi, 13 other muscle hijackers were selected in late 2000 or early 2001. All were from Saudi Arabia, with the exception of Fayez Banihammad, who was from the United Arab Emirates.

Shortly after the attacks the FBI concluded that the majority of the "muscle" hijackers did not know that they were on a suicide mission, as unlike the pilots they had not prepared last wills and testaments or given other indications that they expected their lives to end. According to an audio recording of Osama bin Laden from 2001, the "muscle" hijackers were not in contact with the pilot hijackers and were not told the true nature of their mission until the day of the attacks.

Hijackers: Mohamed Atta (Egyptian), Abdulaziz al-Omari (Saudi Arabian), Wail al-Shehri (Saudi Arabian), Waleed al-Shehri (Saudi Arabian), Satam al-Suqami (Saudi Arabian).

Two flight attendants called the American Airlines reservation desk during the hijacking. Betty Ong reported that "the five hijackers had come from first-class seats: 2A, 2B, 9A, 9C and 9B." Flight attendant Amy Sweeney called a flight services manager at Logan Airport in Boston and described them as Middle Eastern. She gave the staff the seat numbers and they pulled up the ticket and credit card information of the hijackers, identifying Mohamed Atta.