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I have read different explanations for this. Some Catholic writers maintain that St Paul had the stigmata, and so it was Biblical, and not new at all (according to the text cited.) Also, it may be that others did, between the time of St Paul and St Francis, and we do not know of them.

Others claim that veneration of the crucifix - rather than simply an ornate flat cross - was introduced in the medieval period, and this was blessed by the grace of stigmata appearing. The appearance of the crucifix has been controversial in Christianity, and some staunch traditionalists believe that stigmata is a divine sign of approval for this devotion. (One hardly need add the rationalist critique of this, which is that the visual aid is causing imitation.)

A recent article on americancatholic.org takes a moderate position. It says:

Q: Recently, after watching a video about the life of Padre Pio, my husband and I wondered why the wounds appeared in the hands rather than the wrists. The hand sites are found depicted in many traditional paintings, while the wrists are the accepted actual site of the piercing. Could this anomaly be proof of a less-than-miraculous reason for the stigmata?

A: Two reference books shed light on your question. The HarperCollins Encyclopedia of Catholicism, edited by Richard P. McBrien, states, "On very rare occasions the Catholic Church has accepted an occurrence of the stigmata as authentic, but has never defined their origin or nature, thus allowing physical, psychological and preternatural explanations for these phenomena."

Ian Wilson, in Stigmata (Harper & Row, San Francisco), declares, "They [stigmata] are one of the most baffling and intriguing of medical and scientific mysteries."

Obviously, there are few sure answers we can give or find regarding the stigmata. We are not even certain how the stigmata—wounds of the Passion—looked on Christ’s body. We can only speculate. But we do know that the stigmata do not appear the same in all who are believed to have had them.

One stigmatic, for instance, had only the wounds that would have been made by the crown of thorns. Two possessed only the wound in the side. Some had the lance wound in the left side (Padre Pio), another in the right side (St. Francis of Assisi). One had the hand wounds in the wrists, others in the palms of the hands.

Is it significant that more women than men have had the stigmata? What can we conclude from the fact that most stigmatics came from the Dominican and Franciscan Orders? And what does it say that some saints were stigmatics but not all stigmatics were saints?

As I read Wilson, he searches for a natural explanation of the stigmata. Among the possibilities he suggests is some inner mechanism comparable to that which under stress produces evolutionary adaptations in species.

In his study, Wilson notes some stigmatics seem to have identified with earlier stigmatics—ultimately with Jesus. Finally, Wilson notes, "A really riveting feature is the extraordinary precision of the mechanism’s conformity to the visualization that triggered it. Stigmata have been precisely positioned to conform with the wounds of a stigmatic’s favorite crucifix. Or a wound may have taken on the exact shape, such as a cross."

That seems to imply that the stigmata may occur according to the way the subject pictures or imagines them.

For books on the stigmata besides Wilson’s, see: Voices, Visions and Apparitions and They Bore the Wounds of Christ: The Mystery of the Sacred Stigmata, both by Michael Freeze, S.F.O. (Our Sunday Visitor).

"[1] How do Catholic theologians explain the absence of stigmata to the 13th century and a consistent presence of stigmatics in subsequent centuries?"

I don't know if there is any established consensus as to why this may be, but if you will indulge me a few moments, I have some theories. (But I also think SD's suggestion above could be inspired.)

If we said for the sake of argument that the stigmata that Francis received were a genuine manifestation of God's grace, then why might God want such a miracle to occur?

We know from scripture that as well as having compassion on those who fly to Him for aid, God uses miracles to elicit faith or bolster faith. This is especially so in time of crisis for His people.

What article of faith then might God be looking to reinforce by manifestations of stigmata?

One of the greatest threats to God's Kingdom on earth in the early 13th century was the advance of Islam. One of the central heresies of Islam, like the Docetists and Gnostics before them, was that Christ was not crucified and He did not die on the cross. It was principally to combat this heresy that the Catholic Church had previously promoted the use of Crucifixes incorporating the Corpus Christi rather than the simple empty cross.

St. Francis himself was driven by a desire to convert these infidel, to the extent that in June 1219 he allowed himself to be taken captive so that he might preach before Saladin and his Saracen hordes.

Although Francis was not apparently successful with the Saracens, his reception of the stigmata would have had a powerful effect upon any doubting Thomas Christians, who might have been lured by the infidel heresies. Even in modern times as many muslims are drawn to St. Francis, perhaps their discovery of his stigmata will help them to question the source of these and the veracity of the lying Quran?

St. Francis only received the stigmata 5 years after his encounter with Saladin, and his biographer certainly believed it was due to Francis' meditation on Christ's Passion. I dare say that Francis' meditation was aided by the prevalence of the Crucifix as an aid to devotion, and this of course would not have been around early in the first millenium.

The Catholic Encyclopedia recounts his reception of the stigmata as follows:

"Early in August, 1224, Francis retired with three companions to "that rugged rock 'twixt Tiber and Arno", as Dante called La Verna, there to keep a forty days fast in preparation for Michaelmas. During this retreat the sufferings of Christ became more than ever the burden of his meditations; into few souls, perhaps, had the full meaning of the Passion so deeply entered. It was on or about the feast of the Exaltation of the Cross (14 September) while praying on the mountainside, that he beheld the marvellous vision of the seraph, as a sequel of which there appeared on his body the visible marks of the five wounds of the Crucified which, says an early writer, had long since been impressed upon his heart. Brother Leo, who was with St. Francis when he received the stigmata, has left us in his note to the saint's autograph blessing, preserved at Assisi, a clear and simple account of the miracle, which for the rest is better attested than many another historical fact. The saint's right side is described as bearing on open wound which looked as if made by a lance, while through his hands and feet were black nails of flesh, the points of which were bent backward."

"[2] If St. Francis does bear marks in his wrists unlike other stigmatics, why would God (whom I presume causes the marks to appear) place them in differing locations? If they duplicate the marks on Christ there should be consistency I would think."

I am not sure that St. Francis had the nails in his wrists. I would imagine that his stigmata were similar to those found on the San Damiano cross which was one of his principal aids to meditation on Christ's passion. (But I can't remember whether this cross has the stigmata in the palms or the wrists).

If the stigmata do appear in different places in different people, I guess it probably has something to do with what their understanding of Christ's Passion would be.

God is quite aware that we are weak and fallible vessels, and in order to communicate with us effectively He has to speak to us in terms we can comprehend. If my understanding of crucifixion was that of nailing through the palm, and God sent me wounds in my wrists, then being rather dense, I might miss the point of it. Assumimg of course that one of the purposes of the stigmata is to communicate something to us and those around us.