Pepys was a lifelong bibliophile and carefully nurtured his large collection of books, manuscripts, and prints. At his death, there were more than 3,000 volumes, including the diary, all carefully catalogued and indexed; they form one of the most important surviving 17th-century private libraries. The most important items in the Library are the six original bound manuscripts of Pepys' diary, but there are other remarkable holdings, including:[54]
- Incunabula by William Caxton, Wynkyn de Worde, and Richard Pynson
- Sixty medieval manuscripts
- The Pepys Manuscript, a late-15th-century English choirbook
- Naval records such as two of the 'Anthony Rolls', illustrating the Royal Navy's ships c. 1546, including the Mary Rose
- Sir Francis Drake's personal almanac
- Over 1,800 printed ballads, one of the finest collections in existence.[55]
Pepys made detailed provisions in his will for the preservation of his book collection. His nephew and heir John Jackson died in 1723, when it was transferred intact to Magdalene College, Cambridge, where it can be seen in the Pepys Library. The bequest included all the original bookcases and his elaborate instructions that placement of the books "be strictly reviewed and, where found requiring it, more nicely adjusted".
The Ephemera Society emblem uses Pepys' portrait and characterizes him as “the first general ephemerist.”[56] Two large albums of ephemera saved by Pepys are in his library.