Problem: Paul writes, “There was given me a thorn in the flesh, a messenger of Satan to torment me—to keep me from exalting myself!” (2 Cor. 12:7) What is the thorn in the flesh?
Solution: Scholars have speculated for centuries as to what the thorn in the flesh might have been. Here are three of the most common suggestions:
OPTION #1: Sinful temptation
Advocates of this view claim that the phrase “in the flesh” refers to Paul’s sin nature. In 1 Corinthians, Paul sent the unrepentant believer to Satan “for the destruction of his flesh” (1 Cor. 5:5). Since Satan is also mentioned in this context (“…a messenger of Satan to torment me…”), advocates of this view argue that Paul had some sort of sinful temptation that Satan was giving him. However, this perspective doesn’t fit with Paul praying three times for this temptation to be taken away (v.8)—especially in light of passages like 1 Corinthians 10:13, which promises to help us escape temptation. Also, this would mean that God gave Paul this temptation (“…there was given me a thorn in the flesh…”), but this doesn’t fit with James 1:13 which states: “Let no one say when he is tempted, ‘I am being tempted by God’; for God cannot be tempted by evil, and He Himself does not tempt anyone.” For these reasons, we don’t find this a viable option.
OPTION #2: False teachers and opponents
The Greek word for “messenger” (angelos) always refers to a personal being in Paul’s letters—not a physical affliction. In the context of the letter (2 Cor. 10-13), Paul is battling with his adversaries in Corinth. It makes sense that this messenger was a false teacher or opponent of Paul, who was sent from Satan to challenge him (“a messenger of Satan to torment me”). Under this view, his thorn in the flesh would be some sort of persecution from this man, and his “weakness” (astheneia) would be his lack of public esteem in the eyes of the Corinthians (c.f. 1 Cor. 1:25, 27; 4:10)—not a physical sickness.
While this view is plausible, it still doesn’t account for the language of the thorn being in Paul’s “flesh.”
OPTION #3: Physical pain or sickness
Advocates of this view point out that this thorn was “in the flesh.” A straightforward reading of this verse would imply that this was some physical weakness or sickness. This fits with Paul’s beatings that were mentioned immediately in the context (2 Cor. 11:23-29) and the “persecutions” mentioned later (v.10). Moreover, Paul uses the term “weakness” (astheneia) to refer to physical sickness in his other letters (c.f. 1 Cor. 11:30; Gal. 4:13; 1 Tim. 5:23). Most interpreters agree with this third view.
Our view is that a blending of options #2 and #3 are most likely. Paul was probably persecuted by some false teacher and opponent and publicly disgraced. One of these vicious blows to his body wouldn’t heal, and this is what was causing him pain (c.f. Gal. 6:17). He pled that God would take away this painful (and maybe humiliating?) wound, but God let him keep it to humble him. It would have been embarrassing to walk around Corinth with a painful and humiliating wound, but God used this to draw people to Paul’s side and win them over to Christ.
On a final note, God must have kept Paul’s thorn ambiguous for a reason. His thorn in the flesh has been great encouragement to believers down through the centuries, because we don’t know exactly what it was. Harris rightly summarizes, “Had Paul revealed what his [“thorn”] was, Christians of succeeding generations who lacked his particular affliction or disability would have tended to find his experience (vv. 8–10) irrelevant. As it is, countless believers have been helped by his reference to his “thorn.”
 Kruse, C. G. (1987). 2 Corinthians: an introduction and commentary (Vol. 8, p. 199). Downers Grove, IL: InterVarsity Press.
 Harris, M. J. (1976). 2 Corinthians. In F. E. Gaebelein (Ed.), The Expositor’s Bible Commentary, Volume 10: Romans Through Galatians (F. E. Gaebelein, Ed.) (396). Grand Rapids, MI: Zondervan Publishing House.