The difference between pyelonephritis and cystitis is that pyelonephritis is an upper urinary tract infection, while cystitis is a lower urinary tract infection. 2. The routes of infection are different: pyelonephritis is mainly a blood-borne infection, and some are caused by retrograde infection of bacteria in the bladder via the ureter, while cystitis is caused by retrograde infection of bacteria from the urethra into the bladder. Although both have symptoms of urinary tract irritation such as frequent, urgent and painful urination, patients with pyelonephritis also have discomfort such as soreness and pain in the kidney area, while patients with cystitis have no such symptoms.4 Pyelonephritis is often accompanied by symptoms of cystitis, while cystitis can exist alone or can be a retrograde bacterial infection complicating pyelonephritis.