His close friend Padre Agostino wrote in 1915, asking specific questions, such as when he first experienced visions, whether he had been granted the stigmata, and whether he felt the pains of the Passion of Christ, namely the crowning of thorns and the scourging. Pio replied that he had been favoured with visions since his novitiate period (1903 to 1904). Although he had been granted the stigmata, he had been so terrified by the phenomenon he begged the Lord to withdraw them. He wrote that he did not wish the pain to be removed, only the visible wounds, since he considered them to be an indescribable and almost unbearable humiliation.[66]
On 20 September 1918, while hearing confessions, Pio claimed to have had a reappearance of the physical occurrence of the stigmata. The phenomenon was reported to have continued for fifty years, until the end of his life. The blood flowing from the stigmata purportedly smelled of perfume or flowers.[68] He reported to Agostino that the pain remained and was more acute on specific days and under certain circumstances. He also said that he was suffering the pain of the crown of thorns and the scourging. He did not define the frequency of these occurrences but said that he had been suffering from them at least once weekly for some years.[66] Though Pio said he would have preferred to suffer in secret, by early 1919, news had begun to spread. Pio often wore red mittens or black coverings on his hands and feet as he was embarrassed by the marks.[31] However, no visible scarring was present at the time of Pio's death.[69]
In a letter to Padre Benedetto, his superior and spiritual advisor from San Marco in Lamis, dated 22 October 1918, Pio described his experience of receiving the stigmata:
On the morning of the 20th of last month, in the choir, after I had celebrated Mass I yielded to a drowsiness similar to a sweet sleep. [...] I saw before me a mysterious person similar to the one I had seen on the evening of 5 August. The only difference was that his hands and feet and side were dripping blood. This sight terrified me and what I felt at that moment is indescribable. I thought I should have died if the Lord had not intervened and strengthened my heart which was about to burst out of my chest. The vision disappeared and I became aware that my hands, feet and side were dripping blood. Imagine the agony I experienced and continue to experience almost every day. The heart wound bleeds continually, especially from Thursday evening until Saturday. Dear Father, I am dying of pain because of the wounds and the resulting embarrassment I feel deep in my soul. I am afraid I shall bleed to death if the Lord does not hear my heartfelt supplication to relieve me of this condition. Will Jesus, who is so good, grant me this grace? Will he at least free me from the embarrassment caused by these outward signs? I will raise my voice and will not stop imploring him until in his mercy he takes away, not the wound or the pain, which is impossible since I wish to be inebriated with pain, but these outward signs which cause me such embarrassment and unbearable humiliation[71]....the pain was so intense that I began to feel as if I were dying on the cross.[72]
Once made public, the wounds were studied by a number of physicians, some hired by the Vatican as part of an independent investigation. Some claimed that the wounds were unexplainable and never seem to have become infected.[31][73] Despite seeming to heal they would then reappear periodically.[74] Alberto Caserta took X-rays of Pio's hands in 1954 and found no abnormality in the bone structure.[75] Some critics accused Pio of faking the stigmata, for example by using carbolic acid to make the wounds. Maria De Vito (the cousin of a local pharmacist at Foggia) testified that the young Pio bought a little bottle of carbolic acid and four grams of veratrine in 1919.[76]
The bishop of Volterra, Raffaello Rossi considers the accusation concerning carbolic acid and veratridine (veratrine) and he concludes: "[Padre Pio] requested carbolic acid to disinfect syringes needed for shots, and veratridine for ... a prank to be played during recreation!! Padre Pio had experienced the effects of this powder mixed, in an imperceptible dose, in the tobacco offered to him by a Brother. Without knowing anything about poisons, without even considering what veratridine was (and that is why he asked for four grams), he requested it to repeat the joke and laugh at the expense of some Brothers! That's all. Instead of malice, what is revealed here is Padre Pio's simplicity, and his playful spirit."[77][78]
In his 2005 book, Padre Pio and America, however, author Frank Rega claims that the acid was actually used for: "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."[79]
Bishop Raffaello Rossi in his Votum on Padre Pio of Pietrelcina in 1921 adds: "To summarize, what I believe can be certainly affirmed today is that the stigmata at issue are not a work of the devil, nor a gross deceit, a fraud, the trick of a devious and malicious person. I would like to add that his "stigmata" do not seem to me a morbid product of external suggestion."[80]