Says wikipedia:
"His stigmata, regarded by some as evidence of holiness, was studied by physicians whose independence from the Church is not known.[20][21] The observations were reportedly unexplainable and the wounds never became infected.[20][21][38] His wounds healed once, but reappeared.[39] The wounds were examined by Luigi Romanelli, chief physician of the City Hospital of Barletta, for about one year. Dr. Giorgio Festa, a private practitioner also examined them in 1920 and 1925. Professor Giuseppe Bastianelli, physician to Pope Benedict XV agreed that the wounds existed but made no other comment. Pathologist Dr. Amico Bignami of the University of Rome also observed the wounds, but could make no diagnosis.[40] Both Bignami and Dr. Giuseppe Sala commented on the unusually smooth edges of the wounds and lack of edema. Dr. Alberto Caserta took X-rays of the hands in 1954 and found no abnormality in the bone structure.[41]
It was reputed, however, that his condition caused him great embarrassment, and most photographs show him with red mittens or black coverings on his hands and feet where the bleedings occurred.[21] At Padre Pio’s death in 1968, his body appeared unwounded, with no sign of scarring. Allegedly there was report that doctors who examined his body found it empty of all blood.[42]
Historian Sergio Luzzatto and others, both religious and non-religious, have accused Padre Pio of faking his stigmata. Luzzatto’s theory, namely that Padre Pio used carbolic acid to self-inflict the wounds, is based on a document found in the Vatican’s archive — the testimony of a pharmacist at the San Giovanni Rotondo, Maria De Vito, from whom he ordered 4 grams of the acid. According to De Vito, Padre Pio asked her to keep the order secret, saying it was to sterilise needles. The document was examined but dismissed by the Catholic Church during Padre Pio’s beatification process.[43]
One commentator expressed the belief that the Church likely dismissed the claims based on witnesses that stated the acid was in fact used for sterilization: "The boys had needed injections to fight the Spanish Flu which was raging at that time. Due to a shortage of doctors, Padres Paolino and Pio administered the shots, using carbolic acid as a sterilizing agent.”
Some modern research has indicated stigmata are of hysterical origin,[20] or linked to dissociative identity disorders,[21] especially the link between dietary constriction by self-starvation, dissociative mental states and self-mutilation, in the context of a religious belief.[22] Anorexia nervosa cases often display self-mutilation similar to stigmata as part of a ritualistic, obsessive compulsive disorder. A relationship between starvation and self-mutilation has been reported amongst prisoners of war and during famines.[23][24][25] A psychoanalytic study of stigmatic Therese Neumann has suggested that her stigmata resulted from post-traumatic stress symptoms expressed in unconscious self-mutilation through abnormal autosuggestibility.[26]
In his Stigmata: A Medieval Phenomenon in a Modern Age, Edward Harrison suggests that there is no single mechanism whereby the marks of stigmata were produced. Harrison found no evidence from a study of contemporary cases that the marks were supernatural in origin. He concluded, however, that marks of natural origin need not be hoaxes. Some stigmatics marked themselves in attempt to suffer with Christ as a form of piety. Others marked themselves accidentally and their marks were noted as stigmata by witnesses. Often marks of human origin produced profound and genuine religious responses. Harrison also noted that the male-to-female ratio of stigmatics, which for many centuries had been of the order of 7 to 1, had changed over the last 100 years to a ratio of 5:4. Appearance of stigmata frequently coincided with times when issue of authority loomed large in the Church. What was significant about stigmatics was not that they were predominantly men, but that they were non-ordained. Having stigmata gave them direct access to the body of Christ without requiring the permission of the Church through the Eucharist. Only in the last century have priests been stigmatized.[27]
From the records of St. Francis’ physical ailments and symptoms, Dr. Edward Hartung concluded in 1935 that he knew what health problems plagued the holy man. Hartung believed that he had an eye ailment known as trachoma, but also had quartan malaria. Quartan malaria infects the liver, spleen, and stomach, causing the victim intense pain. One complication of quartan malaria occasionally seen around Francis’s time is known as purpura, a purple hemorrhage of blood into the skin. Purpuras usually occur symmetrically, so each hand and foot would have been affected equally. If this were the case of St. Francis, he would have been afflicted by ecchymoses, an exceedingly large purpura. The purple spots of blood may have been punctured while in the wilderness and therefore appear as an open wound like that of Christ.[28]