Why do my kidneys hurt when i wake up in the morning?

Not kidneys: Kidneys are deep seated organs and do not hurt unless it is infected or bleeding or stone passing through the kidneys. if its happening when you wake up , it is unlikely due to kidneys, It is often muscular or skeletal pain in your back.Likely causes- improper posture, poor mattress/bed.Check with your doctor to evaluate for musculoskeletal cause.