The larger part of St. Andrew's remains were apparently stolen from Constantinople in 1210 and these were transported to Amalfi in Southern Italy where they still lie. In 1879 the Archbishop of Amalfi sent a small piece of the Saint's shoulder blade from the Amalfi relics to the re-established Roman Catholic community in Scotland.
On 11 April 1462 the governor of the city of Patras Thomas Palaiologos, the last ruler of Morea and brother of the last Roman Emperor Constantine Palaiologos, left Patras and went to the West, due to the fact that the Turks took over Peloponnesos in 1460. Thomas Palaiologos took with him the Precious Skull of the First-Called Apostle in order to protect it from not falling into the hands of the Turks, and there he handed it over to the Latins to ensure its safety. In return, Thomas was given the Golden Rose, a palace in Rome and an annual allowance of 6,000 ducats. Pope Pius II promised to keep the skull and Thomas safely "as long as danger threatened".
The relic was received with ostentatious signs of devotion. Cardinal Bessarion and two other members of the sacred college received it at Narni and conveyed it to Rome. The pope, accompanied by the remaining cardinals and the Latin clergy, went out to the Ponte Molle to give it welcome. After falling prostrate before the Apostle's skull, Pius delivered an appropriate address in which he congratulated the fragment upon coming safely out of the hands of the Turks to find at last, as a fugitive, a place beside the remains of its brother Apostles. The address being concluded, the procession reformed and, with Pius borne in the Golden Chair, conducted the skull to its last resting-place. The streets were decked in holiday attire, and no one showed greater zeal in draping his palace than Rodrigo Borgia. The skull was deposited in St. Peter's, after, as Platina says, "the sepulchres of some of the popes and cardinals, which took up too much room, had been removed."
The ceremonies were closed by Bessarion in an address in which he expressed the conviction that St. Andrew would join with the other Apostles as a protector of Rome and in inducing the princes to combine for the expulsion of the Turks. In 1462 Pius erected a monument on the site of the Milvian Bridge where the initial ceremonies had taken place: the Tempietto di Sant'Andrea a Ponte Milvio.
While Thomas lived in Rome, he was recognized throughout Christian Europe as the rightful Emperor of the East.* After all, he was the youngest surviving son of the Eastern Roman Emperor Manuel II Palaiologos and his wife Helena Dragaš. After the desertion of his older brother to the Turks in 1460, Thomas Palaiologos became the legitimate claimant to the Roman throne in Byzantium. To create greater support for his situation Thomas changed his religion to Catholicism in his last years of life. The skull of St. Andrew became enshrined in one of the four central piers of Saint Peter's Basilica in the Vatican.
Five hundred years passed. In 1962 the Metropolitan of Patras and the Mayor of Patras made a request to the Pope to have the "treasure of the people of Patras" returned back to them and the place of his martyrdom. Pope Paul VI, in a gesture of good-will, decided to fulfill their request. Removing the skull and a finger of the Apostle Andrew from Saint Peter's Basilica, they were brought to Patras and given over to Metropolitan Constantine of Patras at Trion Symmachon Square (Three Allies) on September 26, 1964. This was a huge celebration for Patras, where thousands attended, including 20 archbishops and President George Papandreas of Greece. A procession brought the Precious Skull to the Church of Saint Andrew where a Doxology was chanted.
Metropolitan Nikodemos of Patras later wrote the history of this event together with the Service of Praise in its honor. This was included in the periodical Ekklesia (15 October 1964, no. 20). In attendance also was the then Archimandrite, later Archbishop of the Greek Archdiocese of America, Demetrios Trakatellis, who translated the sermon for the occasion by Metropolitan Constantine of Patras from Greek to French.
A portion of the encyclical of Metropolitan Constantine reads: "Συγκίνησις δυσπερίγραπτος πληροί τας ψυχάς. Παλμοί ιεροί διατρέχουν την πόλιν. Δάκρυα κυλούν εις τους οφθαλμούς. Επανέρχεται μετά 500 έτη από την Βασιλικήν του Αγίου Πέτρου Ρώμης εις την Βασιλικήν του Αγίου Ανδρέου Πατρών η Τιμία Κεφαλή του Πολιούχου ημών. Ουδέποτε άλλο άγγελμα συνήγειρε βαθύτερον την πόλιν ημών. Εις το βάθος του ορίζοντος εμφανίζονται τα οράματα των Παλαιολόγων, διαγράφει κύκλους ο Βυζαντινός δικέφαλος αετός. Κυματίζει εις την αύραν του Πατραϊκού η σημαία της πόλεως με τον χιαστόν Σταυρόν. Νεανίσκοι και παρθένοι, πρεσβύτεροι μετά νεωτέρων, άρχοντες και πάντες λαοί αινέσωμεν το όνομα Κυρίου. Άσωμεν αυτώ άσμα καινόν."
* In ORTHODOXY ON SALE: THE LAST BYZANTINE, AND THE LOST CRUSADE by Silvia Ronchey of the University of Siena, Italy. Ronchey provides evidence to support a theory that Pius and the Greek leaning cardinals had decided that after a successful Crusade against the Turks, Thomas Palaiologos was to be placed as the legitimate ruler of the re-conquered New Byzantium which was to be under the control of the West. Excerpts can be read here.