What does it mean if your urine is clear when you have a kidney infection?

Maybe....: Maybe you don't actually have an infection after all? If you have pain in your side, burning urination and/or frequency, or blood in the urine, but your urine tests are "clear" (negative), you may not have an infection, but another problem, such as a stone. You may require further testing, such as imaging studies, to pin down your problem.