The Phrase
"A thorn in the side" - a persistent source of irritation or trouble - derives from two biblical passages warning the Israelites about the consequences of failing to expel their enemies. The phrase became one of English's most common metaphors for ongoing, nagging difficulty caused by a particular person or group.
Biblical Origin
Numbers 33:55 contains God's warning to Moses: "But if you do not drive out the inhabitants of the land, those you allow to remain will become barbs in your eyes and thorns in your sides." Judges 2:3 repeats the warning with variation: "I will not drive them out before you; they will become traps for you, and their gods will become snares to you."
The thorn image draws on agricultural experience - the thornbush that catches clothing, scratches skin, and resists removal. Applied to an enemy population, it describes something that cannot be ignored, that draws blood at unexpected moments, and that proves impossible to eradicate. Paul uses a related phrase in 2 Corinthians 12:7, where he mentions "a thorn in my flesh" - which he describes as "a messenger of Satan to torment me." Paul's thorn has been endlessly debated (illness? a spiritual adversary? a persistent sin?) but his use of the image confirms its currency in early Christian discourse.
Semantic Drift
"A thorn in the side" now describes anyone or anything that is a persistent annoyance - a difficult colleague, an inconvenient regulation, a rival who keeps winning. The phrase has lost its military and theological specificity; it simply names chronic irritation. The related "thorn in the flesh" retains slightly more of its Pauline theological weight - it tends to be used of internal rather than external difficulties - but both phrases are now general idioms.
The mobility of the phrase between "side" and "flesh" is itself instructive: both versions circulate freely in English, reflecting the two biblical sources (Numbers/Judges for the side; Paul for the flesh) without speakers generally being aware of the distinction.
Legacy
Like many body-part idioms in English ("a pain in the neck," "get under your skin"), "thorn in the side" converts physical discomfort into relational difficulty. The biblical origin gave it a specific historical and theological context that the idiom has long since left behind. What remains is the precision of the image: not a wound, not an obstacle, but a persistent, minor, inescapable irritant that cannot be removed and will not stop drawing attention to itself.