When a character is injured by a contaminated attack (such as a mummy's slam attack, which can transmit mummy rot), touches an item smeared with diseased matter, or consumes disease-tainted food or drink, he must make an immediate Fortitude saving throw. If he succeeds, the disease has no effect -- his immune system fought off the infection. If he fails, he takes damage after an incubation period. Once per day afterward, he must make a successful Fortitude saving throw to avoid repeated damage. Two successful saving throws in a row indicate that he has fought off the disease and recovers, taking no more damage.
You can roll these Fortitude saving throws for the player so that he doesn't know whether the disease has taken hold.
Diseases have various symptoms and are spread through a number of vectors. The characteristics of several typical diseases are summarized on Table 8-2: Diseases in the Dungeon Master's Guide.
Use of the Heal skill can help a diseased character. Every time a diseased character makes a saving throw against disease effects, the healer makes a check. The diseased character can use the healer's result in place of his saving throw if the Heal check result is higher. The diseased character must be in the healer's care and must have spent the previous 8 hours resting.
Characters recover points lost to ability score damage at a rate of 1 per day per ability damage, and this rule applies even while a disease is in progress. That means that a character with a minor disease might be able to withstand it without accumulating any damage.