Additionally, two American Airlines planes crashed this morning. American Airlines Flight 11, from Boston to Los Angeles, crashed into the North Tower of the World Trade Center just before 9 a.m. ET, and American Airlines Flight 77, heading from Dulles Airport near Washington to Los Angeles, crashed into the Pentagon.
United CEO James Goodwin said: "The thoughts of everyone at United are with the passengers and crew of these flights. Our prayers are also with everyone on the ground who may have been involved."
Goodwin added: "United is working with all the relevant authorities, including the FBI, to obtain further information on these flights."
For the first time ever, the Federal Aviation Administration has ordered all to be flights canceled nationwide.
"This was a measure we took because we thought it was prudent," FAA spokeswoman Laura Brown told reporters.
ABCNEWS' Lisa Stark and Dan Harris contributed to this report.