The remains of St. Francis were solemnly transported to the new church on 25 May 1230. Pope Innocent IV consecrated the basilica on 25 May 1253. Pope Benedict XIV declared the church a Patriarchal Basilica and Papal Chapel on 25 March 1754 with the Constitution "Fidelis Dominus". Pius VII, on 12 September 1818, gave permission to the Minister General of the Friars Minor Conventuals to proceed with the excavations underneath the main altar of the lower basilica in order to find the tomb of St. Francis, which had been conceiled by Brother Elias and then by Pope Eugene IV in 1476.

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