John was born in Illinois in 1953, of Croatian heritage, and has one brother, Danny, and 3 sisters (Amanda, Melissa and Rebecca). His parents (Daniel and Joe Anne) owned and ran a local newspaper in Benton, Illinois (Benton Evening News). His father passed away in 1980.
He attended Benton Consolidated High School, Eastern Illinois University but transferred to Illinois State University because they had a better drama program. In 1976, he quit Illinois State to work at the Steppenwolf Theater in Chicago, which was founded by his friend Gary Sinise.
In the 80s, John was briefly linked to his Dangerous Liaisons co-star, Michelle Pfeiffer. He was married to Glenne Headly (1982-1988), and to Italian Nicoletta Peyran since 1989. He and Nicoletta have 2 children, Amandine (b. 1990) and Lowry (b. 1992). He nows lives with his family in France, though in 2004 they also set up home in Boston.
John Malkovich's Scores