Shepard was born on November 5, 1943, in Fort Sheridan, Illinois. He was named Samuel Shepard Rogers III after his father, Samuel Shepard Rogers, Jr., but his nickname was "Steve Rogers". His father was a teacher and farmer who served in the United States Army Air Forces as a bomber pilot during World War II; Shepard characterized him as "a drinking man, a dedicated alcoholic". His mother, Jane Elaine (nee Schook), was a teacher and a native of Chicago.

When Shepard first arrived in New York City, he roomed with Charlie Mingus, Jr., a friend from his high school days and the son of jazz musician Charles Mingus. He then lived with actress Joyce Aaron. From 1969 to 1984, he was married to actress O-Lan Jones, with whom he had one son, Jesse Mojo Shepard (born 1970). From 1970 to 1971, Shepard was involved in an extramarital affair with musician Patti Smith, who remained unaware of Shepard's identity as a multiple Obie Award-winning playwright until it was divulged to her by Jackie Curtis. According to Smith, "Me and his wife still even liked each other. I mean, it wasn't like committing adultery in the suburbs or something." After ending his relationship with Smith, Shepard relocated with his wife and son to London in the early 1970s. Returning to the U.S. in 1975, he moved to the 20-acre Flying Y Ranch in Mill Valley, California, where he raised a young colt named Drum and used to ride double with his young son on an appaloosa named Cody.  Shepard met Academy Award-winning actress Jessica Lange on the set of the film Frances, in which they were both acting. He moved in with her in 1983, and they were together for nearly 30 years; they separated in 2009. They had two children, Hannah Jane (born 1985) and Samuel Walker Shepard (born 1987). In 2003, his elder son, Jesse, wrote a book of short stories that was published in San Francisco; Shepard appeared with him at a reading to introduce the book.  Despite having a longstanding aversion to flying, Shepard allowed the real Chuck Yeager to take him up in a jet plane in 1982, while preparing to play the test pilot in The Right Stuff. Shepard described his fear of flying as a source for a character in his 1966 play Icarus's Mother. He went through an airliner crash in the film Voyager, and according to one account, he vowed never to fly again after a very rocky trip on an airliner coming back from Mexico in the 1960s.  In the early morning hours of January 3, 2009, Shepard was arrested and charged with speeding and drunken driving in Normal, Illinois. He pled guilty to both charges on February 11, 2009, and was sentenced to 24 months probation, alcohol education classes, and 100 hours of community service. On May 25, 2015, Shepard was arrested again, this time in Santa Fe, New Mexico, for aggravated drunk driving.  His 50-year friendship with Johnny Dark (stepfather to O-Lan Jones) was the subject of the documentary Shepard & Dark (2013) by Treva Wurmfeld. A collection of Shepard and Dark's correspondence, Two Prospectors, was also published that year.

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