It was not a pleasant time to be a patient, but if you valued your life, there was no choice. To relieve the pain, you submitted to more pain, and with any luck, you might get better. Surgeons in the early part of the Middle Ages were often monks because they had access to the best medical literature – often written by Arab scholars. But in 1215, the Pope said monks had to stop practicing surgery, so they instructed peasants to perform various forms of surgery. Farmers, who had little experience other than castrating animals, came into demand to perform anything from removing painful tooth abscesses to performing eye cataract surgery.
Some of the medieval medical graphics may be NSFW. Link -via Gorilla Mask
For example, bloodletting wasn't just performed as a cure for disease, but was undertaken regularly a couple of times a year by healthy people, in order to stave off illness.
And it wasn't just plague victims who were encouraged to confess to cure themselves. EVERYONE was. It was thought that all disease was a direct punishment from God, so to cure ANYTHING, you had to cleanse your soul. Your body would not heal if your soul was still poisoned.
Ancient Greek theories of medicine were the strongest ideas in the field right up to the 18th century and beyond. They placed a huge emphasis on the importance of diet, lifestyle and exercise, environment, excretions, and even your emotional state.