The novel was partly inspired by Stephenson's involvement with the Clock of the Long Now project, to which he contributed three pages of sketches and notes. A separate compact disc, entitled IOLET: Music from the World of Anathem, containing eight experimental vocal compositions by David Stutz, will be sold separately through CD Baby and the Long Now Foundation, with profits going to The Clock of the Long Now project.
To create the world of Arbre, Stephenson constructs new vocabulary. In order to familiarize the reader with the new words, many of which are analogous to English, Latin or Greek words and ideas, he put a glossary at the end of the book. Each chapter begins with a definition of one of these words, which usually relates to the chapter in some way. In addition, the Orth language spoken by the characters was created by Jeremy Bornstein at the author's request, and has been documented. The word anathem was invented by Stephenson, based on the word anthem and the Greek word anathema. In the book, an anathem is a mathic ritual by which one is expelled from the mathic world.