Sinful, wicked, or deeply wrong in a religious or moral sense; also used casually to mean extremely bad or unpleasant.
From Old English 'unhalig,' combining 'un-' (not) with 'halig' (holy). The religious meaning is original; the casual intensifier meaning (as in 'an unholy mess') developed in modern usage.
What's fascinating is how 'unholy' started as a serious religious condemnation but now we use it for everything from 'unholy alliance' (unexpected partnership) to 'unholy loud noise'—the word's intensity made it perfect for exaggeration in casual speech.
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