St. John Chrysostom was buried in Komany. In 438, Proclus, Patriarch of Constantinople (434-447), while celebrating divine services in St. Sophia's Church, uttered a eulogy to the memory of his great teacher, in which he compared St. John Chrysostom with St. John, the Forerunner of the Lord, who preached repentance and also suffered for exposing vices. The people, burning with love for St. John Chrysostom, did not allow the patriarch to finish his word, but began to unanimously ask him to appeal to the emperor with a request for the transfer of the holy relics of the saint from Koman to Constantinople. 
Saint Proclus went to Tsar Theodosius II (408-450) and, on behalf of the Church and the people, asked him about it. The emperor agreed and sent special envoys with a silver shrine to Komany to honorably transport the holy relics. The inhabitants of Koman deeply grieved that they were being deprived of the great treasure, but they could not resist the royal decree. When the imperial envoys went to the tomb of St. John, they could not take his relics. Then the emperor, in repentance, wrote a letter to the saint, asking him for forgiveness for himself and for his mother Eudoxia. This epistle was read at the tomb of St. John, laid on it, and an all-night vigil was celebrated. Then they went to the tomb, easily lifted the relics and carried them onto the ship (the tomb of St. John remained in Komany, near Sukhumi). At the same time, the healing of a poor man who had venerated the veil of the holy sepulcher took place. Upon the arrival of the relics of St. John in Constantinople, on January 27, 438, the whole city, led by Patriarch Proclus, Emperor Theodosius, with all his synclite and many people came out to meet him. Numerous clerics with candles, censers and banners took the silver shrine and brought it to the church of the Holy Martyr Irina with chants. 
When Patriarch Proclus opened the coffin, St. John's body turned out to be incorruptible, and a fragrance emanated from it. Prostrating himself at the tomb, Emperor Theodosius II tearfully asked the saint to forgive his mother. The people did not leave the shrine all day and all night. The next morning, the relics of the saint were taken to the Cathedral Church of the Holy Apostles. When the shrine was placed on the patriarchal throne, the whole people shouted with one mouth: "Accept your throne, Father!" and Patriarch Proclus and many who stood by the shrine saw St. John open his mouth and say "Peace to all!"
In the 9th century, Joseph the Hymnwriter, Cosmas the Vestiator and others wrote hymns in honor of the transfer of the relics of St. John Chrysostom, which are still sung by the Church in memory of this event.
In 1204, during the Fourth Crusade, the relics of the saint were taken from Constantinople to Rome, and on November 26, 2004, by decision of Pope John Paul II, most of the relics of the saint were returned to the Orthodox Church of Constantinople, along with those of Gregory the Theologian, and are kept in St. George's Cathedral in Phanar (Istanbul). Small fragments of the relics of the saints were left in the Vatican.
At least two relics claim to be the head of John Chrysostom, one is kept in the monastery of Vatopedi on Mount Athos, the other in the Cathedral of Christ the Savior in Moscow.
Other parts of the saint's relics are on Mount Athos in the monasteries of Philotheos, the Great Lavra, Dohiar, in the monasteries of Meteora, in the church of St. John Chrysostom in Venice.