In 1969, Klaus Weber, now 72, from Germany visited the Cathedral with five other men, their visit coincided with the organ being refurbished.
According to Klaus, a fellow member of the group, Georg took a fancy to one of the pipes.
He told the Church Times: "They were lined up. Georg took one small pipe. We couldn't stop him. He never said why."
When the group were heading home, Georg was worried that it would be seized by customs at Dover and wanted to throw the pipe away.
Klaus, who was 22 at the time, was adamant they could not throw it away as it was a "historical piece" and offered to take the pipe back to Germany with him for safe keeping, which he did without trouble.
Klaus kept the organ pipe ever since, after not being able to track down Georg to give it to him.
50 years later, Klaus felt it was time to right a wrong and wrote to staff at York Minster offering the 16-inch pipe, a D sharp, plus £50 - £1 for every year it was missing.
A spokesperson for the cathedral said: "It wasn't missed. Unfortunately, it can't go back in the organ; it will go into the collection with a note."
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