I am having pain in my lower right and left side of my back , i get headaches and upset stomach . what could this be ?

Things to consider..: Could be one of many things. It could be a virus that you might be battling, could be a urinary or pelvic infection, and if you are sexually active you need to consider pregnancy, especially if you are late for your period. If a virus it should get better in a few days with rest and plenty of fluids. If not make sure you get evaluated for a final diagnosis.