When a character contracts a disease -- by being 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.
Diseases have various symptoms and are spread through a number of vectors.
Use of the Heal skill will remove the disease upon a successful DC check of 15. However, it will not remove any ability score damage resulting from the disease's effect.  Recuperative spells are needed to repair ability score damage caused by disease.
Ability score drains caused by disease are only cured by a (lesser or better) Restoration spell or Cure Disease. Resting does nothing for it.