Anemia Occurrence: uncommon  Cause: a lack of choleric humors in the food, possibly poisonous earth.
Malaria Occurrence: common Cause: poisonous vapors from swamps
St. Anthony's Fire Occurrence: common Cause: poisonous ground, festering wounds, bad food, foot hair vapors, contact with diseased persons and chickens. Desc.: causes ether uncontrolled muscle spasms or gangrene depending on whether the source was abundant in choleric or phlegm.
Influenza Occurrence: common  Cause: poisonous vapors in the night air (these vapors are suppressed by heat and light)
Small Pox Occurrence: common Cause: vapors from diseased persons. Desc.:childhood disease, all PCs are assumed to have an immunity to it for free.
Black Death Occurrence: rare (outbreaks occur about every twenty years and tend to be localized now) Cause: vapors from diseased persons and animals. Halfling poisonings.
Leprosy Occurrence: uncommon Cause: unclean habits, contact with lepers.
Epilepsy Occurrence: uncommon Cause: head injuries, demonic possession, contact with epileptics and congealing of the blood's humors in the brain.
Sylphs (Natorie Pox) Occurrence: rare Cause: sexual contact, unnatural interference with domestic animals

Chaldean Black Rot Occurrence: none in campaign area Cause: Chaldean sorcerers and demons.  Desc.:Victim rots until they burst into flames
African Yellow Death Occurrence: none in campaign area Cause: Choleric vapors excited by the extreme heat of the southern sun.  Desc.:Victim turns yellow and quickly putrefies. Spreads to any living thing touched.
Scaldian Red Death Occurrence: none in campaign area Cause: vapors from ill sheep Desc.:causes festering scours over victim. Victim's head eventually explodes. Thought to be Divine retribution for sin of the Scaldian habit.

Notes:
While this may sound outrageous and wrong to the 21st Century reader remember this is correct from your character's point of view.