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Cooper was born in Kansas City, Missouri, the son of Mary Ann, a homemaker, and Charles Cooper, who served as a doctor in the United States Air Force and operated a cattle ranch. He has an older brother, Chuck, and grew up as a "blue-collar cowpoke" in Houston, Texas and Kansas City. Mr. Cooper attended Stephens College and the University of Missouri, where he dual majored in the school of agriculture and the school of drama. After graduation, Cooper moved to New York City to pursue his career.

Cooper's early performances include Matewan, the 1987 picture by John Sayles, and the 1989 miniseries Lonesome Dove. Some of his standout[citation needed] performances include Money Train as a psychotic pyromaniac who terrifies toll booth operators, Lone Star in a rare leading role as a Texas sheriff charged with solving a decades old case, and in 1996 John Grisham's book made into a movie directed by Joel Schumacher "A Time to Kill" as Deputy Dwayne Looney American Beauty as a homophobic Colonel of the United States Marine Corps. Cooper won an Academy Award for Best Supporting Actor and a Golden Globe Award in 2003 for playing the role of John Laroche in Adaptation. Cooper also appeared in The Bourne Identity in 2002 as a ruthless CIA special ops director, a role he reprised (in flashbacks) in The Bourne Supremacy. Cooper is often typecast as a government/military character. Cooper was busy in 2005, having appeared in three well-received and acclaimed films: Jarhead (reuniting him with American Beauty director Sam Mendes and October Sky actor Jake Gyllenhaal), Capote and Syriana. He was in the thriller Breach, playing real-life FBI operative and spy Robert Hanssen. Cooper said that his belief was that Breach was the "first studio film where they've considered me the lead" actor. He appeared as a government agent in dangerous territory alongside Jamie Foxx, Jennifer Garner and Jason Bateman in the action thriller The Kingdom.

Cooper resides in Kingston, Massachusetts, with his wife, Marianne Leone Cooper, whom he married in 1983. In 1987, their son Jesse Lanier Cooper was born. Three months premature, Jesse developed a cerebral hemorrhage and cerebral palsy. After searching for the best schools for children with special needs, Cooper and Leone moved to Kingston, Massachusetts, where they became strong advocates for exceptional children. Jesse was eventually mainstreamed into Silver Lake Regional High School, where he became an honor student. On January 3, 2005, Jesse Cooper died from complications of cerebral palsy. A memorial fund was set up in his name, the Jesse Cooper Foundation. Cooper has described his political views as "pretty left of left".