The origins of the Relais San Clemente date back to its Church and were established as a result of a Papal Bull Relais San Clemente a Perugiafrom Pope Gregory VI in 1045 who called it "Ripa fluminis positam cum omnibus earum pertinentis et adiacentis" (located by the bank of the Tiber with all its grounds and buildings). The Catalogue of Churches published by Mariotti indicates that, on this site known as Passo dell'Acqua, there was a Church devoted to San Clemente ("Ecclesia Santi Clementis justa Tiberim"), that regularly paid its Papal taxes.
It is said that famous visitors such as German Emperor Henry III who came to Italy in 1046 was invited by Roman aristocracy to settle the dispute between Silvester III, Gregory VI and Benedicty IX for the Papal throne. He subsequently deposed the three of them in the synods of Sutri and Rome and he then selected a Pope that he trusted, the German Bishop Suidger from Bamberg. As soon as he was elected as Clemente II, he crowned Henry III Emperor.