Before the modern era, cryptography focused on message confidentiality (i.e., encryption)—conversion of messages from a comprehensible form into an incomprehensible one and back again at the other end, rendering it unreadable by interceptors or eavesdroppers without secret knowledge (namely the key needed for decryption of that message). Encryption attempted to ensure secrecy in communications, such as those of spies, military leaders, and diplomats. In recent decades, the field has expanded beyond confidentiality concerns to include techniques for message integrity checking, sender/receiver identity authentication, digital signatures, interactive proofs and secure computation, among others.
The main classical cipher types are transposition ciphers, which rearrange the order of letters in a message (e.g., 'hello world' becomes 'ehlol owrdl' in a trivially simple rearrangement scheme), and substitution ciphers, which systematically replace letters or groups of letters with other letters or groups of letters (e.g., 'fly at once' becomes 'gmz bu podf' by replacing each letter with the one following it in the Latin alphabet). Simple versions of either have never offered much confidentiality from enterprising opponents. An early substitution cipher was the Caesar cipher, in which each letter in the plaintext was replaced by a letter some fixed number of positions further down the alphabet. Suetonius reports that Julius Caesar used it with a shift of three to communicate with his generals. Atbash is an example of an early Hebrew cipher. The earliest known use of cryptography is some carved ciphertext on stone in Egypt (ca 1900 BCE), but this may have been done for the amusement of literate observers rather than as a way of concealing information.
The Greeks of Classical times are said to have known of ciphers (e.g., the scytale transposition cipher claimed to have been used by the Spartan military). Steganography (i.e., hiding even the existence of a message so as to keep it confidential) was also first developed in ancient times. An early example, from Herodotus, was a message tattooed on a slave's shaved head and concealed under the regrown hair. More modern examples of steganography include the use of invisible ink, microdots, and digital watermarks to conceal information.
In India, the 2000-year-old Kamasutra of Vātsyāyana speaks of two different kinds of ciphers called Kautiliyam and Mulavediya. In the Kautiliyam, the cipher letter substitutions are based on phonetic relations, such as vowels becoming consonants. In the Mulavediya, the cipher alphabet consists of pairing letters and using the reciprocal ones.
In Sassanid Persia, there were two secret scripts, according to the Muslim author Ibn al-Nadim: the šāh-dabīrīya (literally "King's script") which was used for official correspondence, and the rāz-saharīya which was used to communicate secret messages with other countries.
David Kahn notes in The Codebreakers that modern cryptology originated among the Arabs, the first people to systematically document cryptanalytic methods. Al-Khalil (717–786) wrote the Book of Cryptographic Messages, which contains the first use of permutations and combinations to list all possible Arabic words with and without vowels.
Ciphertexts produced by a classical cipher (and some modern ciphers) will reveal statistical information about the plaintext, and that information can often be used to break the cipher. After the discovery of frequency analysis, perhaps by the Arab mathematician and polymath Al-Kindi (also known as Alkindus) in the 9th century, nearly all such ciphers could be broken by an informed attacker. Such classical ciphers still enjoy popularity today, though mostly as puzzles (see cryptogram). Al-Kindi wrote a book on cryptography entitled Risalah fi Istikhraj al-Mu'amma (Manuscript for the Deciphering Cryptographic Messages), which described the first known use of frequency analysis cryptanalysis techniques.
Language letter frequencies may offer little help for some extended historical encryption techniques such as homophonic cipher that tend to flatten the frequency distribution. For those ciphers, language letter group (or n-gram) frequencies may provide an attack.
Essentially all ciphers remained vulnerable to cryptanalysis using the frequency analysis technique until the development of the polyalphabetic cipher, most clearly by Leon Battista Alberti around the year 1467, though there is some indication that it was already known to Al-Kindi. Alberti's innovation was to use different ciphers (i.e., substitution alphabets) for various parts of a message (perhaps for each successive plaintext letter at the limit). He also invented what was probably the first automatic cipher device, a wheel which implemented a partial realization of his invention. In the Vigenère cipher, a polyalphabetic cipher, encryption uses a key word, which controls letter substitution depending on which letter of the key word is used. In the mid-19th century Charles Babbage showed that the Vigenère cipher was vulnerable to Kasiski examination, but this was first published about ten years later by Friedrich Kasiski.
Although frequency analysis can be a powerful and general technique against many ciphers, encryption has still often been effective in practice, as many a would-be cryptanalyst was unaware of the technique. Breaking a message without using frequency analysis essentially required knowledge of the cipher used and perhaps of the key involved, thus making espionage, bribery, burglary, defection, etc., more attractive approaches to the cryptanalytically uninformed. It was finally explicitly recognized in the 19th century that secrecy of a cipher's algorithm is not a sensible nor practical safeguard of message security; in fact, it was further realized that any adequate cryptographic scheme (including ciphers) should remain secure even if the adversary fully understands the cipher algorithm itself. Security of the key used should alone be sufficient for a good cipher to maintain confidentiality under an attack. This fundamental principle was first explicitly stated in 1883 by Auguste Kerckhoffs and is generally called Kerckhoffs's Principle; alternatively and more bluntly, it was restated by Claude Shannon, the inventor of information theory and the fundamentals of theoretical cryptography, as Shannon's Maxim—'the enemy knows the system'.
Different physical devices and aids have been used to assist with ciphers. One of the earliest may have been the scytale of ancient Greece, a rod supposedly used by the Spartans as an aid for a transposition cipher. In medieval times, other aids were invented such as the cipher grille, which was also used for a kind of steganography. With the invention of polyalphabetic ciphers came more sophisticated aids such as Alberti's own cipher disk, Johannes Trithemius' tabula recta scheme, and Thomas Jefferson's wheel cypher (not publicly known, and reinvented independently by Bazeries around 1900). Many mechanical encryption/decryption devices were invented early in the 20th century, and several patented, among them rotor machines—famously including the Enigma machine used by the German government and military from the late 1920s and during World War II. The ciphers implemented by better quality examples of these machine designs brought about a substantial increase in cryptanalytic difficulty after WWI.