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Cystitis and urethritis are both inflammatory/infectious processes, but they occur in different locations. Cystitis is an inflammatory/infectious process of the bladder, while urethritis is an inflammatory/infectious process of the urethra.
Cystitis can be caused by infection and is more common in women. Urethritis resulting from infection is often caused by sexually transmitted organisms and is a sign of a sexually transmitted disease such as chlamydia or gonorrhea.