During the American Civil War, what medicine did they have and use? And what diseases did they have?

Infections and diseases were much more deadly than battle in the Civil War, and claimed more lives.  Veterans wrote about a "camp cough" that would happen every morning when the army arose.  Knowledge about germs and sanitation and how disease was spread was limited at the time, which meant that often little was done to prevent or contain epidemics of Typhus, lockjaw, or fevers.  Operating conditions were horrible, with no sanitation of saws in between amputations, little training of the doctors and surgeons, and very limited amounts of painkillers.

Nurses provided cold and hot compresses, cleaned wounds of debris with alcohol, and used alcohol to anesthetize their patients.  In the heat of battlefield surgery, there wasn't time for that, as the limbs piled up and volunteers held down the wounded while their injured limbs and shattered bones were cut away.

Dorothea Dix, the early 1800's reformer, improved sanitation greatly during the war for Union hospitals, mostly just because she was a clean freak, but people noticed that survival rates in her hospitals went up.