Purpose: To report our experience with the use of the botulinum toxin-A (BoNT/A) formulations Botox® and Prosigne® in the treatment of neurogenic detrusor overactivity (NDO). Materials and Methods: At a single institution, 45 consecutive patients with refractory urinary incontinence due to NDO received a single intradetrusor (excluding the trigone) treatment with botulinum toxin type A 200 or 300 units. Botox was used for the first 22 patients, and Prosigne for the subsequent 23 patients. Evaluations at baseline and week 12 included assessment of continence and urodynamics. Safety evaluations included monitoring of vital signs, hematuria during the procedure, hospital stay, and spontaneous adverse event reports. Results: A total of 42 patients were evaluated (74% male; mean age, 34.8 years). Significant improvements from baseline in maximum cystometric capacity (MCC), maximum detrusor pressure during bladder contraction, and compliance were observed in both groups (P < 0.05). Improvement in MCC was significantly greater with Botox versus Prosigne (+103.3% vs. +42.2%; P = 0.019). Continence was achieved by week 12 in 16 Botox recipients (76.2%) and 10 Prosigne recipients (47.6%; P = 0.057). No severe adverse events were observed. Mild adverse events included 2 cases of transient hematuria on the first postoperative day (no specific treatment required), and 3 cases of afebrile urinary tract infection. Conclusions: Botox and Prosigne produce distinct effects in patients with NDO, with a greater increase in MCC with Botox. Further evaluation will be required to assess differences between these formulations.