Since its introduction in the late 1970s for the treatment of strabismus and blepharospasm, botulinum toxin (BoNT) has been increasingly used in the interventional treatment of several other disorders characterized by excessive or inappropriate muscle contractions. Over the years, the number of primary clinical publications has grown exponentially, and still continues to increase. It has been shown that BoNT blocks cholinergic nerve endings in the autonomic nervous system but does not block non-adrenergic non-cholinergic responses mediated by nitric oxide (NO). The present paper reviews a number of recent clinical indications for urological and pelvic floor dysfunctions, such as overactive and neurogenic bladder, non-bacterial prostatitis, benign prostatic hyperplasia, chronic anal fissure, or conditions associated to hyperactivity of the puborectalis muscle during straining. These indications provide a new promising palette of indications for future usage of BoNT in clinical practice.