Sanborn worked with a retiring CIA employee named Ed Scheidt, Chairman of the CIA Office of Communications, to come up with the cryptographic systems used on the sculpture. However, Sanborn omitted the extra letter from small Kryptos models that he sold. Bauer, Link, and Molle suggest that this may be a reference to the Hill cipher as an encryption method for the fourth passage of the sculpture. One of the lines of the Vigenère tableau has an extra character (L). The right-hand side of the sculpture comprises a keyed Vigenère encryption tableau, consisting of 867 letters. There are also three misspelled words in the plaintext of the deciphered first three passages, which Sanborn has said was intentional, and three letters (YAR) near the beginning of the bottom half of the left side are the only characters on the sculpture in superscript. In April 2006, however, Sanborn released information stating that a letter was omitted from this side of Kryptos "for aesthetic reasons, to keep the sculpture visually balanced". The ciphertext on the left-hand side of the sculpture (as seen from the courtyard) of the main sculpture contains 869 characters in total: 865 letters and 4 question marks. The name Kryptos comes from the ancient Greek word for "hidden", and the theme of the sculpture is "Intelligence Gathering". Other elements of Sanborn's installation include a landscaped garden area, a fish pond with opposing wooden benches, a reflecting pool, and other pieces of stone including a triangle-shaped black stone slab.
Several morse code messages are found on these copper sheets, and one of the stone slabs has an engraving of a compass rose pointing to a lodestone. In addition to the main part of the sculpture, Jim Sanborn also placed other pieces of art at the CIA grounds, such as several large granite slabs with sandwiched copper sheets outside the entrance to the New Headquarters Building. The main sculpture contains four separate enigmatic messages, three of which have been deciphered. The characters are all found within the 26 letters of the Latin alphabet, along with question marks, and are cut out of the copper plates. The most prominent feature is a large vertical S-shaped copper screen resembling a scroll or a piece of paper emerging from a computer printer, half of which consists of encrypted text. The sculpture comprises four large copper plates with other elements consisting of water, wood, plants, red and green granite, white quartz, and petrified wood. The main part of the sculpture is located in the northwest corner of the New Headquarters Building courtyard, outside of the Agency's cafeteria.