Kidney stones or pyelitis can cause symptoms of back pain and yellow urine. Kidney stones are stones formed when crystalline objects are deposited in the kidneys over a long period of time. If the stones cut the lining of the renal pelvis and cause bleeding, blood is discharged through the urine causing the urine to look more yellow and darker, and in severe cases, the symptoms of blood in the urine may become apparent. When bacteria infect the bladder from the urethra and continue to infect the kidneys, resulting in pyelitis, the patient will experience symptoms such as back pain and fever.