Most levels contain secrets. At the end of each level, the percentage of secrets found is displayed on the intermission screen.
Secret areas are usually hidden to some extent. In many cases, there is some clue to indicate a secret area, such as an off-color wall that is actually a door. By convention, most stock levels are designed so that it is not necessary to find any of the secret areas to reach the exit. Traditionally, however, secret areas are quite helpful to the player, often containing weapons and large powerups.
A special sector type (type 9) is used to calculate the secrets percentage. The number of type 9 sectors in the level is the total number of secrets. When a player first enters a type 9 sector, the number of secrets found is incremented by one. A secret (or "hidden") area may encompass any number of sectors, but will normally include exactly one sector of type 9 in order to give the secrets percentage a straightforward interpretation. Some source ports use the type 9 sector to trigger an announcement such as "A SECRET HAS BEEN REVEALED" or to play a sound, but the original game does not give any indication until the intermission screen.
Linedefs can also have a "secret" flag bit (bit 5). This flag makes a two-sided linedef appear on the automap in red instead of yellow, that is, just like a single-sided linedef. It is typically used to hide entrances to secret areas on the automap (this happens more often in stock levels than in PWADs), but has nothing to do with the calculation of the secrets percentage.
Occasionally, the word "secret" is used in a colloquial or dictionary sense, to mean any hidden area on a map (irrespective of type 9 sectors). For example, this may occur on Usenet or in documentation written by inexperienced PWAD authors.
In vanilla Doom, a secrets percentage of 0% is ambiguous. Normally, it means the player found none of the secrets, but it could also mean that the level has no secrets to find. Some source ports display 100% in the latter case, to indicate that the player has done as well as possible.