Although not substantial in quantity, the Library"s manuscript collection is extremely significant. 160 manuscripts, 13 of which were severely damaged or destroyed during the Civil War, came from the Colegio Mayor de San Ildefonso and were catalogued by José Villa-Amil y Castro in 1878. 
¨De laudibus Crucis¨ by Rabano Mauro is the oldest manuscript in the Library and was copied in Central Europe, in Carolingian script in the 9th century. Although severely damaged during the Civil War, is also very significant Visigothic Bible from the 10th century.
Another work treasured by the Library is the ¨Libros del Saber de Astronomia¨. This contains various works translated in Arabic language for Alfonso X el Sabio"s royal house. However, this work has suffered considerable mutilation over the centuries.
 Other important mansucripts are the 13th/14th century illustrated copy of the ¨Historias¨ by Jimenez de Rada or the early 15th century  ¨Chronica¨ of friar Martín Polono, written in the Bastarda script font, with French border style and the coat of arms of the Luna family.
  At present, the Library is planning a manuscript catalog that will be based on modern standards.