From a fascinating article by Frank M. Rega.
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Recently, new information about this visit has come to light, according to a new book in Italian published by Padre Pio's Friary, Il Papa e Il Frate, written by Stefano Campanella (1). As reported in this book, the future Pope and future Saint had a very interesting conversation. During this exchange, Fr. Wojtyla asked Padre Pio which of his wounds caused the greatest suffering. From this kind of personal question, we can see that they must have already talked together for some time and had become at ease with each other. The priest expected Padre Pio to say it was his chest wound, but instead the Padre replied, "It is my shoulder wound, which no one knows about and has never been cured or treated." This is extremely significant, not only because it reveals that Padre Pio bore this wound, but because, as far as is known, the future pope is the only one to whom Padre Pio ever revealed existence of this secret wound.
Centuries earlier, Our Lord himself had revealed to St. Bernard of Clairvaux in a vision, that his shoulder wound from carrying the heavy wooden cross caused him his greatest suffering, and that the cross tore into his flesh right up to the shoulder bone.