A side effect is an unintended, negative reaction to a medicine or treatment. If the side effect of a headache medicine is that your ears fall off, then maybe don’t take it.
In medicine, a side effect can be any reaction to a drug that's not its specific intended effect — even if it's positive. There are anti-depressants that have the side effect of suppressing the urge to smoke, and seizure disorder medications that relieve some symptoms of mental illness as well. More common are unpleasant side effects like nausea or dizziness.