Cimino was born in New York City on February 3, 1939. A third-generation Italian-American, Cimino and his brothers grew up with their parents in Old Westbury, Long Island. He was regarded as a prodigy at the private schools his parents sent him to, but rebelled as an adolescent by consorting with delinquents, getting into fights, and coming home drunk. Of this time, Cimino described himself as "always hanging around with kids my parents didn't approve of.

Cimino graduated from Westbury High School in 1956. He entered Michigan State University in East Lansing, Michigan. At Michigan State, Cimino majored in graphic arts, was a member of a weight-lifting club, and participated in a group to welcome incoming students. He graduated in 1959 with honors and won the Harry Suffrin Advertising Award. He was described in the 1959 Red Cedar Log yearbook as having tastes that included blondes, Thelonious Monk, Chico Hamilton, Mort Sahl, Ludwig Mies van der Rohe, Frank Lloyd Wright, and "drinking, preferably vodka."  In Cimino's final year at Michigan State, he became art director, and later managing editor, of the school's humor magazine Spartan. Steven Bach wrote of Cimino's early magazine work:  "It is here that one can see what are perhaps the first public manifestations of the Cimino visual sensibility, and they are impressive. He thoroughly restyled the Spartan's derivative Punch look, designing a number of its strikingly handsome covers himself. The Cimino-designed covers are bold and strong, with a sure sense of space and design. They compare favorably to professional work honored in, say, any of the Modern Publicity annuals of the late fifties and are far better than the routine work turned out on Madison Avenue. The impact and quality of his work no doubt contributed to his winning the Harry Suffrin Advertising Award at MSU and perhaps to his acceptance at Yale."  At Yale, Cimino continued to study painting as well as architecture and art history and became involved in school dramatics. In 1962, while still at Yale, he enlisted in the U.S. Army Reserve. He trained for five months at Fort Dix, New Jersey and had a month of medical training in Fort Sam Houston, Texas. Cimino graduated from Yale University, receiving his BFA in 1961 and his MFA in 1963, both in painting.

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