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The Doctor was awarded the title of 'Favourite Hero' in the list compiled by SFX, beating Firefly's Malcolm Reynolds into second place.
The character has been played by eleven actors since 1963, with Matt Smith the current incumbent of the role.
Other high-ranking characters included Dean Winchester from Supernatural, Star Wars smuggler Han Solo and Ianto Jones from Who spinoff Torchwood.
Meanwhile, Who villain the Master also won top billing in a list of science-fiction's greatest villains. Actors to have played the sinister Time Lord include Roger Delgado, Anthony Ainley, Eric Roberts and most recently John Simm.
The rest of the top five consisted of Star Wars tyrant Darth Vader, Batman nemesis the Joker, Scorpius from Farscape and fellow Who foe Davros.
It was previously announced that Doctor Who villains the Daleks had come top in a poll listing the greatest sci-fi monsters.
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