Purpose: The relative impermeability of the bladder mucosa is due to the glycosaminoglycan layer covering the urothelium and the tight junction of the urothelium. Recently, one of the most popular theories of interstitial cystitis is the penetration of urinary irritants into the suburothelial tissue due to an increased permeability of the urothelium. This study was performed to evaluate the effect of the intravesical heparin treatment on the permeability of bladder mucosa in allergic cystitis. Materials and Methods: Rats were sensitized by intraperitoneal injection of ovalbumin(10mg/ml/kg) given on days 1, 3 and 5. The experiments were performed 4 weeks after the last injection. Controls were run simultaneously with the sensitized animals. Sensitized rats were challenged with intravesical ovalbumin(10mg/ml, 1ml) and control rats received 1ml saline intravesically. Sensitized-antigen challenged group was divided into two subgroups; rats treated with intravesical heparin(5mg/ml in 0.9% NaCl) or those treated with 1ml saline intravesically. Immediately following the intravesical heparin(or saline) treatment, 1ml of 14C-urea was placed into the bladder for two hours. We examined the peripheral blood concentration of 14C-urea at periods up to 120 minutes. Results: There was no 14C-urea present in the blood in control group. There was a progressive increase in the blood level of 14C-urea with time in the sensitized-antigen challenge group. Compared with intravesical saline treatment group, there was less progressive increase in the blood level of 14C-urea with time in the intravesical heparin treatment group. We also measured radioactivity of 14C-urea in the bladder tissues and found significantly lower level of 14C-urea in the bladder tissues from intravesical heparin treatment group than intravesical saline treatment group. Conclusions: This study indicates that immunologically induced cystitis increases bladder mucosal permeability in rats and intravesical heparin treatment decrease the permeability significantly.