Objective: The purpose of this study was to describe the methods of a randomized clinical trial of intra-vesical botulinum toxin for refractory urge urinary incontinence. Methods: Clinical sites of the Pelvic Floor Disorders Network (www.pfdn.org) recruited patients with refractory urge urinary incontinence and urodynamic evidence of detrusor overactivity incontinence (DOI) to a 2:1 placebo controlled cystoscopic injection of botulinum toxin A. Results: The primary outcome is time to failure after first injection, with failure defined as a Patient Global Impression of Improvement (PGI-I) score 4 or greater at least 2 months after the first injection or the commencement of any new treatment at any time after the first injection, or an increased intensity of previously established treatment for DOI. Conclusions: This trial was designed to test the efficacy of intra-detrusor botulinum toxin A for the treatment of refractory urge incontinence. Progress of the trial can be monitored on www.clinicaltrials.gov.