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Background Neurogenic bladder (NGB) dysfunction after spinal cord injury (SCI) is generally irreversible. Preliminary animal and human studies have suggested that initiation of sacral neuromodulation (SNM) immediately following SCI can prevent neurogenic detrusor overactivity and preserve bladder capacity and compliance. We designed a multicenter randomized clinical trial to evaluate the effectiveness of early SNM after acute SCI. Methods/Design The scientific protocol comprises a multi-site, randomized, non-blinded clinical trial. Sixty acute, acquired SCI patients (30 per arm) will be randomized within 12 weeks of injury. All participants will receive standard care for NGB including anticholinergic medications and usual bladder management strategies. Those randomized to intervention will undergo surgical implantation of the Medtronic PrimeAdvanced Surescan 97,702 Neurostimulator with bilateral tined leads along the S3 nerve root in a single-stage procedure. All patients will undergo fluoroscopic urodynamic testing at study enrollment, 3 months, and 1-year post randomization. The primary outcome will be changes in urodynamic maximum cystometric capacity at 1-year. After accounting for a 15% loss to follow-up, we expect 25 evaluable patients per arm (50 total), which will allow detection of a 38% treatment effect. This corresponds to an 84 mL difference in bladder capacity (80% power at a 5% significance level). Additional parameters will be assessed every 3 months with validated SCI-Quality of Life questionnaires and 3-day voiding diaries with pad-weight testing. Quantified secondary outcomes include: patient reported QoL, number of daily catheterizations, incontinence episodes, average catheterization volume, detrusor compliance, presence of urodynamic detrusor overactivity and important clinical outcomes including: hospitalizations, number of symptomatic urinary tract infections, need for further interventions, and bowel and erectile function. Discussion This research protocol is multi-centered, drawing participants from large referral centers for SCI and has the potential to increase options for bladder management after SCI and add to our knowledge about neuroplasticity in the acute SCI patient. Trial registration ClinicalTrials.gov # NCT03083366 1/27/2017.