The people had to be forcibly removed from the Church. The body was buried at night.
Bellarmine and others had the remains of Aloysius put into a wooden coffin. Usually this was not done, as most remains were put into a vault alone. But the Father General agreed that Aloysius should be separated.
A flood caused by the overflowing of the Tiber seven years later brought Aloysius' remains back into the public. Fr. Acquaviva ordered the coffin opened. The Provincial, Fr. Bernardine Rossignoli, distributed on this occasion a considerable number of relics, and thus portions of the bones were carried by Fr. Nicholas Lancisius to Poland, and by Fr. Francis Corso to India. The College at Brussels received a shoulder-blade of the Saint, part of which was afterwards sent to Antwerp. The rest was again put into a coffin and this time put higher up in the vault.
The body was translated a few other times afterwards. The head of the Saint was at first given by Father General Acquaviva to the Professed House at the Gesù, but afterwards handed over to the Saint’s brother for the Church of the Jesuit College at Castiglione, where it is still venerated.
In 1626, four years after his canonization, work on the Church of Saint Ignatius began on the site of the old Church of the Annunziata. There a new and magnificent chapel was dedicated to St. Aloysius. To this chapel the holy relics were carried in procession, headed by the General, Fr. Thyrsus Gonzalez, and deposited under the altar on the 20th of December 1699. This was the sixth and last translation, and there the sacred remains rest to this day.
The Jesuit College at Palermo obtained possession of the lower jaw-bone of the Saint; Cologne received the crucifix that he had used during his life and at his death. It was presented by Cardinal Lugo to General Goswin Nickel, who bequeathed the treasure to the College at Cologne on the 26th of May 1661.
Aloysius is attributed with many miracles after his death. The first of which was with his mother. Rudolph was shot dead two years after Aloysius' death. He was excommunicated before his death after being accused of coining false papal money. Only the tears of Martha enabled her son to be buried with the rites of the Church, as the Pope granted her wish. But these events took a toll on the Saint's mother. She was already given her Last Rites when Aloysius appeared to her. She immediately healed and also witnessed the Marquisate's growth under Aloysius' brother, Francis, just as the Saint had predicted to her.
There are many other accounts of Aloysius healing family members and Jesuits. For example, one lay-brother could not kneel during prayer, as Aloysius always had, because of a disease in his knee. After praying to the Saint and promising to say an Our Father and a Hail Mary to him every day, his knee was healed.
But the first miracle the Church recognized in the beatification of Aloysius occurred in 1600. Carmelite nun Catherine de Carlinis (April 8th 1600) was suffering from cancer. She lived in the same convent that Fr. Cepari had given the Life of the Saint to, and also where St. Mary Magdalen de Pazzi had the famous vision of St. Aloysius' glory in heaven. A relic of the Saint ended Catherine's pain. The Superioress elected to go ahead with surgery to remove the cancer regardless. Catherine begged the Saint to reveal his full glory and then fainted from a severe pain. She awoke and was found to be completely healed.
Fr. Cepari knew of 206 miracles. There was such an abundance that not all of them were verified because more than enough were proven for beatification.
One miracle that may still be found today (Fr. Meschler's book claims that it could be found in 1911) is in a Church in Naples known as Gesù vecchio. The Church there possesses a bottle with the Saint's blood. According to Meschler, from the first Vespers of the Feast of St. Aloysius till the second Vespers of the Octave the blood in the little bottle becomes fluid and of a fresh red color. The relic is then usually placed on the altar of St. Aloysius, and the miracle takes place without its being touched, after a few prayers have been recited before the picture of the Saint. Sometimes the blood liquefies unexpectedly at other times of the year as well.
St. Aloysius was canonized on on December 31, 1726.