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.