Your scruples are what keep you from doing things you consider to be morally or ethically wrong. Your scruples won't allow you to cheat on a test, or steal from your brother's Halloween candy stash.
The noun scruple comes from a Latin word, scrupulus, which means a small, sharp stone. Some say that the philosopher Cicero first used the word analogously to compare a worry to a small, sharp stone in your shoe that bothers you. From there the word scruple took on the ethical principles meaning. If you are doing something bad, your scruples will bother you — but emptying your shoe probably won't help.