No one knows for sure what Paul meant when he spoke of the thorn in his flesh when he writes in the New Testament of the Holy Bible:
And to keep me from being too elated by the abundance of revelations, a thorn was given me in the flesh, a messenger of Satan, to harass me, to keep me from being too elated.

2 Corinthians 12:7(NRSV)

Saint Paul's thorn in the flesh 1 has also been identified with epilepsy by some biblical scholars. It's unlikely that this would have been idiopathic epilepsy in view of the late onset in his life, but its clear temporal relationship to an out of the body experience 2, possibly induced by the severe trauma of one of his many beatings or stonings, 3 would suggest that post traumatic epilepsy cannot be ruled out.

Other researchers remark that it may have been carnal temptations while another rebuts that was truly not the case and suggests it was a chronic humiliating malady with acute attacks, such as marsh fever.

A biblical dictionary interprets the thorn not as an illness at all, but to mean persecution by former colleagues. Yet another comments that the passage from the Holy Bible might refer to a psychic or physical ailment which, by Jewish tradition, would be caused by Satan or a demon. Only to further try to explain the thorn in Pauls' flesh as really suggesting an external personal source of affliction; that in the Old Testament thorns meant enemies and that the thorn is the hostility he was certainly facing during his ministries coming from within his own communities, specifically Corinth.

Paul prayed three times for the removal of his thorn. His first two petitions went unanswered. At his third entreaty, however, the Lord protests: ‘sufficient for you is My grace, for My power in infirmity is being perfected.4 The sharp affliction which he had to bear, over and above the normal burden of life was placed upon him to aid in his ministries to come. Paul was flogged and stoned and was ill, but never claimed that these experiences were due to spiritual agencies. Only the truth, that he suffered physically at the hands of unbelieving men, and from the destructive conditions under which the human body exists.

Many phrases have become so common in English speech, and are hardly thought of as Biblical at all. By today's standards thorn in the flesh has become an idiom which means a constant nuisance.

Sources:

McKenzie,John. Dictionary of the Bible
O’Connor, Jerome Murphy . New Jerome Biblical Commentary
O’Curraoin, Tomas. New Commentary on Holy Scripture
The Oxford Companion to the Bible, 1993.