Introduction: Impaired barrier function of bladder epithelium and subsequent infiltration of urine contents are the supposed initial events in the pathophysiology of interstitial cystitis (IC). Altered urinary GAG levels have been suggested as markers for IC, such as hyaluronan (HA) and sulfated GAG (S-GAG), and GAG replacement therapy is one of the main therapeutic approaches for IC. We evaluated urinary GAG behavior and bladder inflammation after intravesical protamine sulfate (PS) injury, simulating IC. Material & Methods: Cystitis was induced in adult female Wistar rats (n=7) by bladder instillation of PS (10 mg). Controls (n=5) were instilled with saline. Urine was collected during 24 hs in a metabolic cage. The rats were sacrificed at days 1 to 7, 10 and 14 after the PS instillation and their bladders were removed for morphometric and biochemistry analysis. HA and S-GAG were measured in all groups and in non-manipulated rats (day 0) by a non-competitive fluorescence-based assay and by a micro electrophoresis technique, respectively, and normalized to creatinine. Additionally, [³⁵S]-inorganic sulfate was intraperitoneally injected in rats (cystitis and control) on days 0, 1, 5 and 7 to assess S-GAG turn over. Results: Compared to controls, neutrophils were increased on the first 2 days and lymphocytes on the 5^th to 7^th days (p<0.05). Both urinary HA and S-GAG had increased levels on the first days and after the 5^th day, with a maximum level on 7^th day. Urine analysis after [³⁵S]-sulfate incorporation revealed a peak of S-GAG on the 5^th and especially on 7^th day, compared to day 0 and their respective controls, suggesting an increased GAG turn over during this period. Conclusions: There were 2 peaks of urinary HA and S-GAG excretion after intravesical PS instillation. The first peak probably correlates to inactivation of native bladder GAG, increased epithelial permeability and desquamation. Based on the higher incorporation of [³⁵S]-sulfate during the second raise, we may assume there was de novo synthesis of GAG, concomitant to the occurrence of lymphocyte inflammatory infiltrate. This phenomenon could be a natural response to either the inflicted damage or the resultant inflammation in order to regenerate the bladder epithelial barrier. Increased levels of S-GAG in the urine of IC patients might represent this response. However, this regeneration process seems somehow to be impaired in patients with IC. Supported by: FAPESP and CNPq.