This is an incomplete list of some of the manuscripts from the Cotton library that today form the Cotton collection of the British Library. Some manuscripts were destroyed or damaged in a fire at Ashburnham House in 1731, and a few are kept in other libraries and collections.

Robert Bruce Cotton organized his library in a room long by six feet wide filled with bookpresses, each with the bust of a figure from classical antiquity on top. Counterclockwise, these were Julius Caesar, Augustus, Cleopatra, Faustina, Tiberius, Caligula, Claudius, Nero, Galba, Otho, Vitellius, Vespasian, Titus, and Domitian. (Domitian had only one shelf, perhaps because it was over the door). In each press, each shelf was assigned a letter; manuscripts were identified by the bust over the press, the shelf letter, and the position of the manuscript (in Roman numerals) counting from the left side of the shelf. Thus, the Lindisfarne Gospels, Nero B.iv, was the fourth manuscript from the left on the second shelf (shelf B) of the press under the bust of Nero. For Domitian and Augustus, which had only one shelf each, the shelf letter was left out of the press-mark. The British Museum retained Cotton's press-marks when the Cotton collection became one of the foundational collections of its library, so manuscripts are still designated by library, bookpress, shelf, and number (even though they are no longer stored in that fashion). For example, the manuscript of Beowulf is designated Cotton MS Vitellius A.xv, and the manuscript of Pearl is Cotton MS Nero A.x.

Augustus iTwo large portfolios containing a 138 16th century maps, charts and plans of towns, buildings, fortifications and related items. Some of the items are plans for projects that were never completed. ii A portfolio containing a collection of 136 mostly Anglo-Saxon charters, also contains a few later medieval charters, Papal Bulls, and some other items. Includes: Item 3 The Ismere Diploma; Item 106 Magna Carta: Exemplification of 1215 iii A collection of drawings, maps and diagrams from the reign of Henry VIII; prints belonging to or associated with the Speculum Romanae Magnificentiae iv Troy Book by John Lydgate, edition of 1555 with some variations. According to heraldic evidence the manuscript was created between 1411 and 1458, probably during Lydgate's lifetime. v Le Trésor des Histoires. Universal history, from the Creation to Pope Clement VI (died 1352). 15th century copy, lavishly illuminated. vi Le livre des propriétés des choses, translated from Latin to French by Jehan Corbechon under the patronage of Charles V of France. 14th century, illuminated. vii Cartulary of Lewes Priory, now catalogued as Cotton MS Vespasian F XV.

Caligula A.iReligious miscellanyA.iiFos. 3–5, A Pistil of Susan (fragment), probably by Huchoun; fos. 5–13, Sir Eglamour of Artois; fos. 22–35, Octavian; fos. 35–42, Sir Launfal; fos. 42–57, Lybeaus Desconus; fos. 71–6, Emaré; fos. 130–4, Sir Isumbras.Mills, M (Ed). 1969. Lybeaus Desconus. Oxford University Press for the Early English Text Society. 302 pp. Middle English romances in British Library MS Cotton Caligula A.ii, p 1.A.iiiTexts on the CarthusiansA.ivAnnals of Eutychius, Patriarch of Alexandria. Text in Arabic.A.vDisputacion de la Felicite Humaine (1st quarter of the 16th century)A.viHumphrey Llwyd, Chronicle of Welsh history, Cadwaladr ap Cadwallon (d. 664 × 682) to AD 1293; notes on the descent of Welsh nobles (1559) A.vii Heliand A.viii Miscellany: some hagiographies, and amongst others, the Libellus de Primo Saxonum vel Normannorum Adventu and Historia Brittonum (attributed to Nennius) A.ix The Owl and the Nightingale; Layamon, BrutA.xPeter of Ickham, De gestis Britonum et Anglorum, to AD 1289 (4th quarter of the 13th century); Chronicle of Worcester Cathedral Priory to 1377, religious miscellanyA.xiRobert of Gloucester, Chronicle; Short Metrical Chronicle of England (imperfect) (2nd half of the 13th century); William Langland, The Vision of Piers Plowman (B version) (1st half of the 15th century), De uita monachorum (Mid 13th century)A.xiiAnnalistic chronicle, AM 1–AD 1246 (Mid 13th century); Cartulary of Pipewell Abbey (3rd quarter of the 13th century – 4th quarter of the 15th century)A.xiiiList of the kings of England from Stephen (1135–1154) to Henry VII (1485–1509) (15th century); Chronicle of English history, AM 1–AD 1347 (4th quarter of the 14th century-1534); Cartulary of Pipewell Abbey (3rd quarter of the 13th century – 4th quarter of the 15th century) A.xiv Caligula Troper A.xv Jerome, De viris illustribus and Vita Sancti Pauli; extracts from Isidore of Seville, Etymologiae; extract from Cyprian, Ad Quirinum Testimonia, book iii; computistical texts; and Easter tables. (1) fos. 3-117, 8th and 9th-century material from France, which had arrived in England by the 9th or 10th century (2) fos. 120–53, once part of BL Egerton 3314, belonging to the 11th century. It consists of two parts: fos. 120–41, part A, computistical texts; annals of Christ Church, Canterbury; Old English and Latin prognostications and charms fos. 142–53, excerpts from Bede, De temporibus anni, with additional notes. At f. 123v is found a pagan Norse charm, invoking the god Thor.A.xviMartinus Polonus, Chronicle (1st half of the 14th century-2nd half of the 15th century); Coluccio Salutati, Epistole (1st half of the 15th century)A.xviiSermon on the murder of Elizabeth Dorrocott committed by William Dillon; report of the murder of Elizabeth Dorrocott, 24 May 1589, and the suicide of William DillonA.xviiiThe Great Roll (Parliamentary Roll or Bannerets' Roll); hymn for the Blessed Virgin Mary; Ingratitude of the great; En un verger m’en entray; Une dame de mult grant pris (imperfect); The treason of Sir Thomas de Turberville; The Song of Caerlaverock (1st quarter of the 14th century) B-E Correspondence, records, and papers, including both originals and copies, concerning England, Scotland, and France. Largely 16th century. Includes letters from Mary, queen of Scots (B.iv, C.iii, C.vii), the correspondence of James VI, King of Scots (C.ix)

Claudius