The long-running series filmed a special episode to mark the occasion at Alexandra Palace in London yesterday.
The Queen, writing in the programme given to audience members, described the show as a "remarkable achievement" and said it "delivered hope, comfort and joy to millions".
"[The series is] a traditional and much-loved part of our Sundays," she said. "I hope this evening's event will be a great occasion."
The birthday episode of Songs of Praise will feature performances from Katherine Jenkins, Andrea Bocelli and LeAnn Rimes.
The show is due to air on BBC One on October 2.
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