The legendary moment when Dylan was heckled with a cry of "Judas" at a 1966 concert will be shown for the first time in the film.
No Direction Home tells the story of Dylan in his key creative years from 1961 to 1966 and shows the famously private singer-songwriter talking about his childhood, relationships and music.
The film also features previously unseen footage of Dylan's live performances, as well as interviews with fellow artists whose lives were closely intertwined with his own, including Allen Ginsberg and Joan Baez, with whom he was romantically involved.
In a broadcasting first, the three-and-a-half-hour film will be shown consecutively over two days on the BBC in the UK and on the American public service broadcasting network, PBS.
Scorsese, who describes himself as a "great fan", did not meet Dylan during the making of the film, preferring to keep a distance from his subject, who gave him complete control over the final cut.
Dylan's manager Jeff Rosen conducted the interview, which lasted 10 hours over a week in 2000, although it has taken the notoriously perfectionist Scorsese until now to complete the film.
It is not the first time Scorsese has filmed Dylan. In 1978, the director of Goodfellas and The Aviator made The Last Waltz, a film about the farewell concert of The Band, which featured Dylan.
Scorsese said: "I had been a great fan for many years when I had the privilege to film Bob Dylan for The Last Waltz. I've admired and enjoyed his many musical transformations. For me, there is no other musical artist who weaves his influences so densely to create something so personal and unique." A major theme of the film is the outrage expressed by fans of his acoustic folk music when he introduced an electric rock sound to his concerts.
The "Judas" moment was at a concert on 17 May, 1966 at Manchester's Free Trade Hall, when after playing an acoustic folk set in the first half, Dylan introduced his band and turned electric.
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Scorsese was granted access to rare film, tape and stills from the Bob Dylan archive, including Murray Lerner's film Festival documenting Dylan's performances at the Newport Folk Festivals from 1963 to 1965 and D A Pennebaker's 1967 documentary Don't Look Back, based on the singer's tour of Britain.
The documentary will be shown on BBC2 on 26 and 27 September as part of the Arena strand, which is celebrating its 30th anniversary this year. Anthony Wall, the Arena series editor, said the film was not just a history of Dylan, but a chronicle of the 1960s.
"Martin Scorsese said he wanted it to be as much a story of the times as the story of Dylan," Mr Wall said. "To see the moment when 'Judas' is actually screamed at him is quite disconcerting." At the time, Dylan responded to the "Judas" cry with a blistering performance of "Like A Rolling Stone". Since then, several people have claimed responsibility for the notorious shout.
Mr Wall added: "Every night, all over the country, he'd do the acoustic half of the set and everybody would say 'genius' and then bring on the group who became The Band, and they were very, very loud.
"They were like the first modern rock band. Fifty per cent of the audience every night went along and jeered and booed.
"Nineteen-sixty-one till 1966 was a very turbulent time. Scorsese seems to take this going into electric as a metaphor for the way the decade changes."
Last year, Dylan, now 65, published his memoirs, Chronicles Vol.1, tracing the early years of the man who started life as Robert Zimmerman.
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