The purpose of this study was to investigate the effect of botulinum toxin type A on bladder function and histology in a rat chemical cystitis model. The study included 41 female Sprague-Dawley rats with chemical cystitis induced by intravesical instillation of hydrochloric acid. The acid instillation was repeated monthly to maintain chronic inflammation. The treatment group (n=21) received 2-3 units of botulinum toxin type A injected into the bladder detrusor at the 3, 6, 9 and 12 o'clock positions, and the control group (n=20) underwent saline injection into the bladder detrusor at the same positions. Urodynamic studies were performed in all rats before the treatment and at death. The rats were killed at 1 week, 2 weeks, 1 month and 2 months after treatment. The bladders were removed and examined histologically for mast cells and inflammatory changes. The cystometric findings showed that, at the beginning and end of the experiment, the increases in the maximum bladder capacity and compliance were significantly higher in the treatment group than in the control group (P=0.000 and P=0.025, respectively). The histological studies revealed similar mast cell counts and leukocyte infiltration for the treatment and control groups. In conclusion, in this rat chemical cystitis model, botulinum toxin type A injected into the bladder detrusor led to a functional improvement. Thus, botulinum toxin type A injection may be an alternative, minimally invasive choice to other surgical treatment options in the treatment of a chronic inflammatory condition to improve deteriorated bladder function.