As an old man, Adso of Melk recounts how, in 1327, as a young Franciscan novice (a Benedictine one in the novel), he and his mentor, Franciscan friar William of Baskerville, traveled to a Benedictine abbey in northern Italy where the Franciscans were to debate with Papal emissaries the poverty of Christ. The abbey boasts a famed scriptorium where scribes copy, translate or illuminate books. The monk Adelmo of Otranto —a young but famous manuscript illuminator— was suspiciously found dead on a hillside below a tower with only a window which cannot be opened. The abbot seeks help from William, who is renowned for his deductive powers. William is reluctantly drawn in by the intellectual challenge and his desire to disprove fears of a demonic culprit. William also worries the abbot will summon officials of the Inquisition if the mystery remains unsolved.
William quickly deduces that Adelmo committed suicide, having jumped from a nearby tower having a window, and that the slope of the hill caused the body to roll below the other tower. William’s solution briefly allays the monks’ fears, until another Monk is found dead, ominously floating in a vat of pig’s blood. The victim is Venantius, a translator of Greek and the last man to speak with Adelmo. The corpse bears black stains on a finger and the tongue. The translator’s death rekindles the monks’ fears of a supernatural culprit, fears reinforced when the saintly Fransciscan friar Ubertino of Casale warns that the deaths resemble signs mentioned in the Book of Revelation. In the scriptorium, William inspects Adelmo’s desk, but is blocked by Brother Berengar, the assistant librarian. Brother Malachia, the head librarian, denies William access to the rest of the building.
William encounters Salvatore, a demented hunchback, and his protector, Remigio da Varagine, the cellarer. William deduces that both were Dulcinites, members of a heretical, militant sect that believes that clergy should be impoverished. William does not suspect them of murder though, since Dulcinites target wealthy bishops, not poor monks. Nevertheless, Remigio’s past gives William leverage in learning the abbey’s secrets. Salvatore tells William that Adelmo had crossed paths with Venantius on the night that Adelmo died. Meanwhile, Adso encounters a beautiful semi-feral peasant girl who has sneaked into the abbey to trade sexual favours for food, and is seduced by her.
Returning that night to Venantius’s desk, William finds a book in Greek, and also a parchment with Greek writing, smudges of a color blended by Adelmo for illuminating books, and cryptic symbols written by a left-handed man using invisible ink. Berengar sneaks into the darkened scriptorium, distracts William and steals the book.
Berengar is later found drowned in a bath and bearing stains similar to those on Venantius. William narrates his conclusions that Adelmo’s death was indeed suicide, due to giving in to Berengar’s requests for homosexual favors. Venantius received a parchment from Adelmo before Adelmo’s death, and Berengar is the only left-handed man in the abbey. William theorizes that the translator transcribed the Greek notes on the parchment from a book, and that the book is somehow responsible for the deaths. The abbot is unconvinced and, burning the parchment, he informs William that the Inquisition — in the person of Bernardo Gui, an old adversary of William — has already been summoned.
Determined to solve the mystery before Gui arrives, William and Adso discover a vast, hidden library above the scriptorium. William suspects the abbey hid the books because much of their contents comes from pagan philosophers. Gui finds Salvatore and the peasant girl fighting over a black cockerel while in the presence of a black cat. For Gui, this is irrefutable proof of witchcraft, and he tortures Salvatore into a false confession. Privately, William reveals his past connection to Gui, and his own past as an inquisitor to Adso. Years earlier, Bernardo Gui demanded that William condemn a man whose sole crime was translating a Greek book that conflicted with the scriptures. Ultimately, Gui had William imprisoned and tortured to change his verdict, with the translator being burned at the stake.
As both William’s Franciscan brothers and the Papal delegates arrive, the debate begins. Soon, the abbey’s herbalist finds a book written in Greek in his dispensary, and is overheard telling this to William. The herbalist returns to his dispensary, only to be murdered by a hooded figure.
Shortly afterwards, Malachia warns Remigio to escape, as Salvatore has revealed their Dulcinite history. After Remigio attempts to escape, Malachia wipes blood from his own shoes, revealing that it was he who murdered the herbalist. Before Remigio can escape the abbey, he is caught by Bernardo Gui’s guards. Learning of Remigio’s Dulcinite past, Gui arrests him for the murders, and brings Remigio, Salvatore and the girl, before a tribunal. Remembering William, Gui chooses him to join the abbot as a tribunal judge. At trial, Remigio proudly admits his past but denies having killed anyone in the abbey. While the abbot quickly condemns Remigio for murder, William points out that the murders are tied to the Greek book, which Remigio could not read, and warns that Remigio’s execution will not end the murders. Under Gui’s threats of torture, however, Remigio “confesses” by falsely summoning the Devil. Gui arranges for the prisoners to be burned at the stake, while William, having “relapsed”, will be taken to Avignon. The Papal delegates condemn the Franciscans for William’s obstinacy, and end the debate.
As the monks prepare to burn Gui’s prisoners, Malachia is found dying, with black stains on his tongue and finger. Although Malachia’s death vindicates William’s warning, Gui takes it as proof that William is the murderer, and orders his arrest. Fleeing Gui’s guards, William and Adso re-enter the secret library and come face to face with the Venerable Jorge, the oldest denizen of the abbey. Having decoded the lines on the translator’s parchment, William demands that Jorge turn over the book that the dead men had been reading: Aristotle’s Second Book of Poetics on Comedy. Jorge hates laughter, thinking it undermines faith in God, and a book on laughter written by Arisotle will only bring laughter to the wise men, and undermine the faith among those of learning. To prevent that, Jorge killed those who had read the book by poisoning its pages. Jorge gives the book to William, thinking he too will suffer the poison. When William reveals that he is wearing gloves, Jorge grabs the book, then starts a blaze that quickly engulfs the library. William stays behind, trying to save some of the books and encouraging Adso to leave. Jorge kills himself by consuming the poison-coated pages.
Seeing the fire, the monks abandon the prisoners, allowing the local peasants to save the girl, though Salvatore and Remigio die. Adso chases Gui, who manages to escape him, but the peasants push his wagon off a cliff, impaling him. As William and Adso depart, Adso encounters the girl, stops for a few seconds, but eventually chooses to go with William. The much older Adso states that he never regretted his decision, as he learned many more things from William before their ways parted. He also says that the girl was the only earthly love of his life, although he never learned her name.