And the popular carol, God Rest Ye Merry Gentlemen, also has an uncertain future, because the word "gentlemen" means that it breaches political correctness.
Both appear in a list, which is published today, of 200 hymns that have been recommended for exclusion. The Church of Scotland's ruling general assembly in Edinburgh is due to discuss the list later this month, with the intention of publishing a new hymn book some time before 2000. The current version was published in 1973.
Hymns face the axe on three possible grounds: "obsolescence"; "exclusivity, or obscure language", and "obtuse or outdated theology".
Jerusalem was felt to be obsolete, said the secretary of the hymnary, the Rev Charles Robertson.
"The tune is wonderful, but there are problem with the words. Most people who sing it don't know what the words mean," he explained.
The hymn's "dark Satanic mills" refer not to the industrial revolution, but to the universities of Oxford and Cambridge, which the poet William Blake regarded as promoting teaching opposed to religion," he said.
"Even if it's a very good tune, it has to offer more than meaningless words."
The first line of God Rest Ye Merry Gentlemen alone placed the hymn on the "exclusion" list, with the hymnary feeling that the word "gentlemen" excluded many people singing the hymn.
Unlike the Catholic Church and the Church of England, whose hymn books are compiled by publishers, the Scottish Church's hymn book is vetted along doctrinal lines..
The committee says that it is willing to listen to any pleas for particular hymns to be spared, but the appeals must be soundly based.
"A request for a hymn to be retained on the basis that it was the favourite of the petitioner's grandmother would not carry the same weight as a request for retention on the basis that the text is the only one in the present hymnary which deals with a particular theological, biblical, devotional or humanitarian issue," said a spokesman.