The origins of the Relais San Clemente date back to its Church and were established as a result of a Papal Bull from 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. Later on a Benedictine Monastery was built around the Church and on 4 February 1331 Federuccio di Guelfone was appointed as a guardian by the Abbot Ugolino di Montevibione of the Benedictine Monastery of San Pietro in Perugia and in 1339 Ser Maffeo from Perugia was appointed Rector. In fact, it was the Abbot of that Monastery who appointed the Rector and the monks who supervised the upkeep of the Church of San Clemente and the cultivation of the surrounding lands in accordance with the Benedictine motto, "Prayer and Work". Historical sources also indicate that under the initiative of the Monastery of San Pietro in Perugia a wooden bridge was built over the Tiber to connect the isolated location with the nearby settlements. In 1437 Pope Niccolò V assigned the Church to Cardinal Orsini; in 1443 Passo dell'Acqua was then transferred under the control of Prior Antonio di Francesco who in turn made it subject to the authority of Don Gigliotto di Giovanni in 1451.