Below is a list of illnesses, parasites, and other ailments mentioned or encountered in Source:MLP and its surrounding universe.
Allergies During the episode Bridle Gossip one of the possible causes Twilight Sparkle considers to explain what turns out to be the effect of poison joke is an allergic reaction.
-Clydesdale fur blight
Its name is similar to a real disorder called dysentery.
Mane and tail loss
The trots In the real world, the trots are simply known as a case of very bad diarrhea.
Blue flu In Three's A Crowd, Discord fakes having come down with blue flu due to inadequate "hoof and claw washing" to get Twilight Sparkle and Princess Cadance to care for him as part of an elaborate prank. Among his faked symptoms are cerulean-hued skin and fur, and sneezing that sends the afflicted flying backwards; he additionally casts a random spell on any nearby object whenever he sneezes, such as burning up a tree's leaves in blue flames or blowing away an entire house. Discord claims the disease is highly contagious as Applejack and Rarity become afflicted after he sneezes on them, turning their coats blue within seconds. According to Discord, besides dozens of outlandish treatments, the blue flu can be cured with a magical soothing elixir brewed from a gargantuan "exquisite magic flower" that grows on a hill at the edge of Equestria, picked as it drops its petals at sunset.
"Cutie pox" is featured in the eponymous episode The Cutie Pox, which Twilight Sparkle describes from a book: "This puzzling pony plague afflicted a population of ponies back in the Paleopony Period! Random cutie marks appeared all over the ponies' bodies, causing them to perform all the talents that came with them! The cause of the breakout was never discovered, and the cutie pox disappeared as mysteriously as they arrived!" Apple Bloom contracts cutie pox in the episode after an overdose of Heart's Desire plant petals. The pox is cured by the flower that grows from the Seeds of Truth supplied by Zecora, which sprout only in the presence of a truthful confession.
This affliction is implied to be exclusive to dragons, and a natural part of their biology.
King Sombra's curse
-Acting like a dog