A number of ciphers were in use in the Middle Ages, including the Alphabetum Kaldeorum.
It has been argued that the Voynich Manuscript is in cipher.
The Wikipedia page on the subject is [1].
References[]
- The Astronomicum page on medieval cryptography is here.
- The Ciphers of the Monks: A Forgotten Number-notation of the Middle Ages, David A. King Franz Steiner Verlag, 2001 (The Times Higher Education review is here - subscription required)
- Traefik Labs page here
A British Library blog page on cracking a medieval code is here.