I think it is rather evident what Paul's thorn was: a messenger from Satan. Now, we could get into a huge discussion about this, but I've heard and think that the thorn was an evil spirit that caused troubles and riots and persecution wherever Paul went. I think its a good idea to read both chapters and think about it. Here it is in the New Living Translation:
2 Corinthians 11
Paul and the False Apostles 1 I hope you will put up with a little more of my foolishness. Please bear with me. 2 For I am jealous for you with the jealousy of God himself. I promised you as a pure bride
[a] to one husband—Christ. 3 But I fear that somehow your pure and undivided devotion to Christ will be corrupted, just as Eve was deceived by the cunning ways of the serpent. 4 You happily put up with whatever anyone tells you, even if they preach a different Jesus than the one we preach, or a different kind of Spirit than the one you received, or a different kind of gospel than the one you believed. 5 But I don’t consider myself inferior in any way to these “super apostles†who teach such things. 6 I may be unskilled as a speaker, but I’m not lacking in knowledge. We have made this clear to you in every possible way.
7 Was I wrong when I humbled myself and honored you by preaching God’s Good News to you without expecting anything in return? 8 I “robbed†other churches by accepting their contributions so I could serve you at no cost. 9 And when I was with you and didn’t have enough to live on, I did not become a financial burden to anyone. For the brothers who came from Macedonia brought me all that I needed. I have never been a burden to you, and I never will be. 10 As surely as the truth of Christ is in me, no one in all of Greece
[b] will ever stop me from boasting about this. 11 Why? Because I don’t love you? God knows that I do.
12 But I will continue doing what I have always done. This will undercut those who are looking for an opportunity to boast that their work is just like ours. 13 These people are false apostles. They are deceitful workers who disguise themselves as apostles of Christ. 14 But I am not surprised! Even Satan disguises himself as an angel of light. 15 So it is no wonder that his servants also disguise themselves as servants of righteousness. In the end they will get the punishment their wicked deeds deserve.
Paul’s Many Trials 16 Again I say, don’t think that I am a fool to talk like this. But even if you do, listen to me, as you would to a foolish person, while I also boast a little. 17 Such boasting is not from the Lord, but I am acting like a fool. 18 And since others boast about their human achievements, I will, too. 19 After all, you think you are so wise, but you enjoy putting up with fools! 20 You put up with it when someone enslaves you, takes everything you have, takes advantage of you, takes control of everything, and slaps you in the face. 21 I’m ashamed to say that we’ve been too “weak†to do that! But whatever they dare to boast about—I’m talking like a fool again—I dare to boast about it, too. 22 Are they Hebrews? So am I. Are they Israelites? So am I. Are they descendants of Abraham? So am I. 23 Are they servants of Christ? I know I sound like a madman, but I have served him far more! I have worked harder, been put in prison more often, been whipped times without number, and faced death again and again. 24 Five different times the Jewish leaders gave me thirty-nine lashes. 25 Three times I was beaten with rods. Once I was stoned. Three times I was shipwrecked. Once I spent a whole night and a day adrift at sea. 26 I have traveled on many long journeys. I have faced danger from rivers and from robbers. I have faced danger from my own people, the Jews, as well as from the Gentiles. I have faced danger in the cities, in the deserts, and on the seas. And I have faced danger from men who claim to be believers but are not.
[c] 27 I have worked hard and long, enduring many sleepless nights. I have been hungry and thirsty and have often gone without food. I have shivered in the cold, without enough clothing to keep me warm.
28 Then, besides all this, I have the daily burden of my concern for all the churches. 29 Who is weak without my feeling that weakness? Who is led astray, and I do not burn with anger?
30 If I must boast, I would rather boast about the things that show how weak I am. 31 God, the Father of our Lord Jesus, who is worthy of eternal praise, knows I am not lying. 32 When I was in Damascus, the governor under King Aretas kept guards at the city gates to catch me. 33 I had to be lowered in a basket through a window in the city wall to escape from him.
2 Corinthians 12
Paul’s Vision and His Thorn in the Flesh1 This boasting will do no good, but I must go on. I will reluctantly tell about visions and revelations from the Lord. 2 I
[a] was caught up to the third heaven fourteen years ago. Whether I was in my body or out of my body, I don’t know—only God knows. 3 Yes, only God knows whether I was in my body or outside my body. But I do know 4 that I was caught up
[b] to paradise and heard things so astounding that they cannot be expressed in words, things no human is allowed to tell. 5 That experience is worth boasting about, but I’m not going to do it. I will boast only about my weaknesses. 6 If I wanted to boast, I would be no fool in doing so, because I would be telling the truth. But I won’t do it, because I don’t want anyone to give me credit beyond what they can see in my life or hear in my message, 7 even though I have received such wonderful revelations from God. So to keep me from becoming proud, I was given a thorn in my flesh, a messenger from Satan to torment me and keep me from becoming proud.
8 Three different times I begged the Lord to take it away. 9 Each time he said, “My grace is all you need. My power works best in weakness.†So now I am glad to boast about my weaknesses, so that the power of Christ can work through me. 10 That’s why I take pleasure in my weaknesses, and in the insults, hardships, persecutions, and troubles that I suffer for Christ. For when I am weak, then I am strong.
Paul’s Concern for the Corinthians 11 You have made me act like a fool—boasting like this.
[c] You ought to be writing commendations for me, for I am not at all inferior to these “super apostles,†even though I am nothing at all. 12 When I was with you, I certainly gave you proof that I am an apostle. For I patiently did many signs and wonders and miracles among you. 13 The only thing I failed to do, which I do in the other churches, was to become a financial burden to you. Please forgive me for this wrong! 14 Now I am coming to you for the third time, and I will not be a burden to you. I don’t want what you have—I want you. After all, children don’t provide for their parents. Rather, parents provide for their children. 15 I will gladly spend myself and all I have for you, even though it seems that the more I love you, the less you love me.
16 Some of you admit I was not a burden to you. But others still think I was sneaky and took advantage of you by trickery. 17 But how? Did any of the men I sent to you take advantage of you? 18 When I urged Titus to visit you and sent our other brother with him, did Titus take advantage of you? No! For we have the same spirit and walk in each other’s steps, doing things the same way.
19 Perhaps you think we’re saying these things just to defend ourselves. No, we tell you this as Christ’s servants, and with God as our witness. Everything we do, dear friends, is to strengthen you. 20 For I am afraid that when I come I won’t like what I find, and you won’t like my response. I am afraid that I will find quarreling, jealousy, anger, selfishness, slander, gossip, arrogance, and disorderly behavior. 21 Yes, I am afraid that when I come again, God will humble me in your presence. And I will be grieved because many of you have not given up your old sins. You have not repented of your impurity, sexual immorality, and eagerness for lustful pleasure.