Objects ranging from ancient Roman sarcophagi to works by Titian, Leonardo da Vinci and Damien Hirst go on display today at the Royal Scottish Academy Building in Edinburgh.
The exhibition, Choice: 21 years of Collecting for Scotland, shows how the inspirational and flamboyant if occasionally controversial leadership of Sir Timothy has transformed the collections of the galleries - despite there being little money for him to purchase with.
It was a curious feeling, he said yesterday, knowing that it was his last show in charge. "You feel triumphant because you're so thrilled it's been done, but you feel a huge nostalgia that you're never going to do it again," he said.
"It was jolly difficult acquiring them. I was walking around with my former chairman the other day and he said, 'It's not like writing out cheques. Each one is a battle honour.' There have been lots of struggles in trying to acquire these things."
The highlights of the show are the high points of Sir Timothy's tenure. They include Botticelli's The Virgin Adoring the Sleeping Christ Child, bought for £10m in 1999, and Venus Anadyomene by Titian, bought from the Duke of Sutherland in 2003 for £11.6m.
Another is Canova's Three Graces statue, which was bought jointly with the Victoria and Albert Museum in London in 1994 after a vigorous public fundraising campaign, during which Sir Timothy had to apologise to the Getty family. He had suggested there was a family feud after one Getty supported the British bid to match funds to stop it going to the J Paul Getty Museum in Los Angeles.
Despite some failures, such as not securing any works by Michelangelo for Scotland, his legendary charm and networking skills have secured gifts and donations that have helped make the galleries institutions of international stature.
"I've had a wonderful time. Of course I've had problems that go with running any big institution but there have been a lot of triumphs and a lot of successes," he said.
"The National Galleries of Scotland had always been an extremely distinguished but quite modest operation. I hope that in the last 21 years we have become more international."
But he fears for the future as rising art market prices make it harder to keep important works in the UK. "I'm worried about the vast quantities of works of art leaving our shores," he said.
He admitted to being a little disappointed that he never got the chance to run the Victoria and Albert Museum or the National Gallery in London, but said: "The pay-off is that I have been able to see through a vision."
An internationally acclaimed scholar, Sir Timothy said he had several books to write, including one "odd but erudite" investigation into the relationship between fine and applied arts from 1400 to 1850.
He intends to continue living in Scotland, where he took up his post in 1984 having previously run Manchester City Galleries, but will also spend time in Italy.
David Barrie, director of the National Art Collections Fund, which is supporting two final acquisitions under Sir Timothy's supervision, said: "In the last 21 years, Sir Timothy Clifford has had an amazing record of achievement in building the collections of the galleries."
Choice: 21 Years of Collecting for Scotland, sponsored by GNER and the Friends of the National Galleries of Scotland, runs from today until 23 January next year. Admission is free.
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