The covers were printed and bound by Polestar Petty as an A/B/C/D split to give retailers four covers to choose from.
More than 1.1m issues of the magazine were printed and distributed to six different TV regions across the UK.
Publisher BBC Magazines produced equal numbers of all 21, except for the David Tennant version, which appeared in the south of England, London and Scotland.
"We know how popular David Tennant is with readers, so we adjusted our print run accordingly," said BBC Magazines head of communications Sarah Williams.
Radio Times head of production Sharon Thompson said the 21 covers were a first. "I thought the eight covers we produced for our Live 8 edition in 2007 was pushing the boundaries, but obviously not."
Neil Dunning, customer services director at Polestar Petty, said: "We are delighted to have been involved with this creative treatment, which draws on our experience in producing split covers."
Polestar has also produced split versions of Radio Times' Doctor Who and Beijing Olympics editions.
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