Botulinum toxins (BoNTs) are known for their ability to potently and selectively modulate neurotransmission for successful long-term treatment of muscle hypercontractility. Recent studies suggest that BoNT has effects on modulation of sensory processing, inflammation and glandular function. Urologists and urogynaecologists have become interested in the potential application of BoNTs in patients with lower urinary tract symptoms, including detrusor and sphincter overactivity, bladder hypersensitivity, interstitial cystitis/painful bladder symptoms and benign prostatic hyperplasia. We review the biological action of BoNT in bladder and prostate, and present the techniques and results of the clinical studies with BoNT in the lower urinary tract.