Toms conscience is getting to him so badly that he becomes ill.  The book goes on about how Aunt Polly is always ordering different painkillers and books on healing.  She uses these things on Tom in attempt to make him feel better.  From what I understood, Tom got hooked on this painkiller stuff and was taking it a lot.  One time his cat was with him so he gave it some of the pain killer.  The cat freaked out and literally started bouncing off walls.  Tom laughed his head off, but was later scolded by his aunt.