The blonde numbers queen, who took over when Carol Vorderman left the show in 2009, had been unaware that she had reached the milestone until host Nick Hewer made the announcement.
And the 27-year-old was even more stunned when Giggs, who recently reached the landmark of 1000 appearances for club and country, popped up and presented her with a flowers and a signed shirt.
Good surprise? Ryan Giggs went to the Countdown
studio to present Rachel Riley with a Manchester United shirt to mark
her 1,000th show
'As Nick continued, I thought they might have got me a bunch of flowers. But I nearly fell through the floor when Ryan Giggs suddenly appeared with some!'
Clearly shocked and pleased about the former Wales captain's presence, Rachel hugged and kissed Giggs to thank him for the gesture.
Pro: Riley had been fully focused on her job until Giggs' intervention
Warm welcome: Giggs' presence and the gesture was clearly appreciated
'I'm really privileged to have a job that I love working on and on such an iconic show. I can't thank the team and Ryan enough for such an amazing surprise.
'My signed "Riley 86" shirt will be taking pride of place at home.'
Future career? Giggs knows all about the pressure of performing on the big stage
Passionate: Riley is a lifelong United fan
Giggs' appearance on the show is due to draw questions about exactly what the sportsman will do upon retirement. At 39 years of age, he remains an effective and important Premier League player but he cannot go on forever.
Many believe him ideally suited to coaching or management - he has already been pictured studying for a coaching course by former team-mate Gary Neville - and with Wales and Manchester United both bound to pose an interest that appears the obvious route.
All smiles: Giggs was also clearly enjoying himself
Glamorous: Riley has long been established on
Countdown, and took over from Carol Vorderman as the maths whizz on the
show back in 2009