An excerpt from Cryptonomicon was originally published in the short story collection Disco 2000, edited by Sarah Champion and published in 1998.
Stephenson's subsequent work, The Baroque Cycle, provides part of the backstory to the characters and events featured in Cryptonomicon. An excerpt of Quicksilver, Volume One of The Baroque Cycle, is included in later prints of the Mass Market Paperback edition.
The Baroque Cycle, set in the late 17th and early 18th centuries, features ancestors of several characters in Cryptonomicon, as well as events and items which affect the action of the later-set book. The subtext implies the existence of secret societies or conspiracies, and familial tendencies and groupings found within those darker worlds.
The short story "Jipi and the Paranoid Chip" appears to take place some time after the events of Cryptonomicon. In the story, the construction of the Crypt has triggered economic growth in Manila and Kinakuta, in which Goto Engineering, and Homa/Homer Goto, a Goto family heir, are involved. The IDTRO ("Black Chamber") is also mentioned.
Peter Thiel states in his book Zero to One that Cryptonomicon was required reading during the early days of PayPal.