Royal items stolen from the The Thistle Chapel include an ornamental tassel from the Queen's ceremonial cushion, and a highly decorated hanging curtain commissioned by the Queen's father George VI.
Other items stolen include a ceremonial seat cover showing the Knight of the Thistle (the highest Scotland chivalry award), a Dutch collection plate from dating back 200 years ago, and an altar cloth.
Four previous monarchs and hundreds of thousands of people have visited The Thistle Chapel since its creation in 1911. The chapel is notable for depicting angels playing bagpipes.
The Very Reverend Professor Iain Torrance, one of the Queen's chaplains and the Dean of the Order of the Thistle, said: "I am very saddened indeed that someone would stoop so low as to steal from this holy place.
"It would be a great pity if, for security reasons, access to this historic and beautiful chapel had to be permanently restricted.
"Temporarily, at least, it has been closed while we assess the situation."
A Police Scotland spokesman has urged anyone with information to come forward.