Ive seen many try to answer this question most with no success at all (coconut did an good job). the fact is the scripture is clear as to exactly what the thorn in the flesh was. It was the persecutions that he was suffering for Christ and the gospel. It is right there in the passage.
Remember there were not chapters or verses when Paul wrote his letter. Look what he says in chapter 11.
2 Cor 11
[SUP]16 [/SUP]I say again, let no man think me a fool; if otherwise, yet as a fool receive me, that I may boast myself a little.
[SUP]17 [/SUP]That which I speak, I speak it not after the Lord, but as it were foolishly, in this confidence of boasting.
[SUP]18 [/SUP]Seeing that many glory after the flesh, I will glory also.
[SUP]19 [/SUP]For ye suffer fools gladly, seeing ye yourselves are wise.
[SUP]20 [/SUP]For ye suffer, if a man bring you into bondage, if a man devour you, if a man take of you, if a man exalt himself, if a man smite you on the face.
[SUP]21 [/SUP]I speak as concerning reproach, as though we had been weak. Howbeit whereinsoever any is bold, (I speak foolishly,) I am bold also.
[SUP]22 [/SUP]Are they Hebrews? so am I. Are they Israelites? so am I. Are they the seed of Abraham? so am I.
[SUP]23 [/SUP]Are they ministers of Christ? (I speak as a fool) I am more; in labours more abundant, in stripes above measure, in prisons more frequent, in deaths oft.
[SUP]24 [/SUP]Of the Jews five times received I forty stripes save one.
[SUP]25 [/SUP]Thrice was I beaten with rods, once was I stoned, thrice I suffered shipwreck, a night and a day I have been in the deep;
[SUP]26 [/SUP]In journeyings often, in perils of waters, in perils of robbers, in perils by mine own countrymen, in perils by the heathen, in perils in the city, in perils in the wilderness, in perils in the sea, in perils among false brethren;
[SUP]27 [/SUP]In weariness and painfulness, in watchings often, in hunger and thirst, in fastings often, in cold and nakedness.
[SUP]28 [/SUP]Beside those things that are without, that which cometh upon me daily, the care of all the churches.
[SUP]29 [/SUP]Who is weak, and I am not weak? who is offended, and I burn not?
[SUP]30 [/SUP]If I must needs glory, I will glory of the things which concern mine infirmities.
[SUP]31 [/SUP]The God and Father of our Lord Jesus Christ, which is blessed for evermore, knoweth that I lie not.
[SUP]32 [/SUP]In Damascus the governor under Aretas the king kept the city of the damascenes with a garrison, desirous to apprehend me:
[SUP]33 [/SUP]And through a window in a basket was I let down by the wall, and escaped his hands.
Now compare the emboldened portion to what he says about the thorn in the flesh in chapter 12
2 Cor 12
[SUP]7 [/SUP]And lest I should be exalted above measure through the abundance of the revelations, there was given to me a thorn in the flesh, the messenger of Satan to buffet me, lest I should be exalted above measure.
[SUP]8 [/SUP]For this thing I besought the Lord thrice, that it might depart from me.
[SUP]9 [/SUP]And he said unto me, My grace is sufficient for thee: for my strength is made perfect in weakness. Most gladly therefore will I rather glory in my infirmities, that the power of Christ may rest upon me.
[SUP]10 [/SUP]Therefore I take pleasure in infirmities, in reproaches, in necessities, in persecutions, in distresses for Christ's sake: for when I am weak, then am I strong.
Seems pretty clear to me