The area has been inhabited since antiquity as evidenced by traces of Etruscan and Roman remains in the lowlands along the river. The name of the village ‘Carfinianum’ suggests that the land had been owned by a Roman dominus called Carfinius.
But the first documented reports date back to medieval times when a settlement was formed around a castle by the Baglioni family.
The village was founded around the thirteenth century when the Captain and Podesta (chief magistrate) of Viterbo, Pandolfo of Anguillara, conquered the largest possible number of castles removing them from Orvieto. Once appropriated Graffignano and the Baglioni had to submit to Viterbo.
So, in 1282 Graffignano went to Viterbo and during the fourteenth century it knew the despotic rule of the Prefects of Vico, who took advantage of the transfer of the Popes to Avignon.
When the Pope returned to Rome, Graffignano was returned to the Baglioni family aid as a reward given to the Church.
The Baglioni were allied with the Orsini of Orvieto and were disliked by the locals. To win the hearts of the people, after the Orsini pope’s death, the Baglioni befriended Viterbo but, as an immediate consequence, were excommunicated from the Church by Pope Martin IV. Forgiveness of the church, requested for many years by the citizens of Graffignano, came only in 1332 thanks to John XXII who gave back the fiefdom under homeland rule.
The fifteenth and sixteenth centuries were characterized by continuous disputes within the family and ended with the intervention of Pope Adrian VI (1522 – 1523) who confiscated the fiefdom. In 1531 the possessions were returned by Pope Clement VII.
In the early seventeenth century the estate was inherited by Countess Domitilla Cesi, whose family had founded the Accademia dei Lincei in Rome. The countess brought to Graffignano devotion to St. Filippo Neri, patron with San Martino Vescovo, and instituted the feast of Our Lady of Sorrows with the related Compagnia dei Sette Dolori.
In 1669 the estate passed to the Borromeo family, which spread the cult of San Carlo Borromeo, and in 1741 it passed to the Roman Prince Scipione Publicola Santa Croce who gave back new life to the area.