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We compared the efficacy and safety of trigonal injections of onabotulinumtoxinA and saline in patients with bladder pain syndrome/interstitial cystitis.This phase II study enrolled women who had had bladder pain syndrome/interstitial cystitis for more than 6 months and pain for 4 months or longer on a visual analogue scale of 0 to 10, which were refractory to common treatment. OnabotulinumtoxinA 100 U in 10 or saline as placebo in 9 was administered as 10 trigonal injections of 1 ml. The primary study end point was the change from baseline pain intensity reported at week 12. Additional end points included O'Leary-Sant scores, micturition frequency, quality of life at week 4, 8 and 12, and the treatment benefit scale at week 12. Safety assessments included urinary tract infection, post-void residual urine and the initiation of clean intermittent catheterization.At week 12 onabotulinumtoxinA had significantly reduced pain compared with saline (mean ± SD –3.8 ± 2.5 vs –1.6 ± 2.1, p <0.05). The proportion of patients who achieved a 50% or greater reduction in the pain visual analog scale was 60% for onabotulinumtoxinA vs 22% for placebo. OnabotulinumtoxinA significantly improved O'Leary-Sant scores and quality of life over placebo at weeks 4, 8 and 12. Important numerical reductions in voiding frequency were also observed with the toxin. OnabotulinumtoxinA was well tolerated. Urinary tract infections developed in 3 patients who received onabotulinumtoxinA vs 2 who received saline. Mean post-void residual urine at week 12 was 5 ± 13 ml for onabotulinumtoxinA vs 0 ml with saline. This study had the limitations inherent to a single center trial with a small number of patients enrolled.OnabotulinumtoxinA 100 U caused significant and clinically relevant improvements in bladder pain and quality of life in patients with bladder pain syndrome/interstitial cystitis refractory to common therapy. It was also well tolerated.