Urinary interleukin-6 (IL-6) has been proposed as a sensitive and specific inflammatory marker in bladder pain syndrome/interstitial cystitis (BPS/IC). We therefore investigated the presence of urinary IL-6 in patients with BPS/IC to find a possible correlation with the symptoms before and after glycosaminoglycan substitution therapy. Urinary IL-6 levels of 25 BPS/IC patients were assessed semi-quantitavely (Milenia Quickline) before and after intra-vesical glycosaminoglycan substitution therapy. Patients received therapy twice weekly with 300 mg pentosanpolysulphate for 5 weeks. Responders were treated for another 5 weeks, whilst non-responders received 40 mg hyaluronic acid weekly for another 10 weeks instead. Treatment response was assessed by the visual analogue scale (VAS) for quality of life and O'Leary-Saint Symptom and Problem Index (OSPI) before, during the 5th week of the treatment and 1 week after the treatment. Before treatment, measurable IL-6 was found in urine samples from 9 out of 25 patients. After treatment, urinary IL-6 was detected in two patients only. The average VAS and OSPI scores before the treatment were 7.9 (4-10) and 25.4 (12-37), respectively. After the treatment, the average VAS and OSPI scores dropped to 5.5 (0-10) and 14.7 (1-29), respectively. No statistically significant difference was found between patients with and without urinary IL-6 and the VAS and OSPI scores before and after the treatment. The urinary IL-6 level in BPS/IC patients is neither suited as a diagnostic marker nor as a predictor of responses to therapies. For the future, it would be important to clarify whether there are subsets of patients with diseases of different aetiologies.