Etymology

fly in the ointment

fly in the oint·ment

Today it means: Something (especially a minor thing) which ruins or spoils everything else, or makes it less pleasant; a nuisance or problem; a disagreeable or unpleasant detail. Full definition →

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The story

A reference to Ecclesiastes 10:1 in the Bible (King James Version; spelling modernized): “Dead flies cause the ointment of the apothecary to send forth a stinking savour: so doeth a little folly him that is in reputation for wisdom and honour.”

Etymology from Wiktionary, CC BY-SA 4.0.