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Several hypotheses regarding the pathophysiology of interstitial cystitis/bladder pain syndrome (IC/BPS) have been put forward, but no consensus has yet been reached. It is suggested that cytokines are involved in IC/BPS, as well as in inflammatory autoimmune diseases. Examining various biomarkers of bladder tissue, including mast cells is underway. However, few reports on a consistent immune activity profile are available. The aim of the study was to assess the cytokine profile, counts of mast cells and plasma cells as well as their relationship in patients with IC/BPS with and without Hunner’s lesions. 44 women with Hunner’s lesions (group I) and 82 women with non-ulcer type (group II) were examined. Patients were questioned on the Pelvic Pain Symptom Scale, Urinary Frequency Scale (PUF), Visual Analogue Scale (VAS) and O’Leary–Santa Interstitial Cystitis Symptom Index (ICSI). Cystoscopy and hydrodistension of the bladder were performed under general anesthesia. In biopsies of the bladder wall, the number of plasma cells and mast cells was assessed, in urine — IL-1β, IL-6, IL-8, TNFα. Statistical processing of the results was carried out using the Statistica 6 software (StatSoft, USA). The Student’s t-test, Spearman’s correlation coefficient were calculated. In patients with Hunner's ulcer, there was an insignificant increase in the scale indices and decreased magnitude for average volume, urination frequency, and maximum emptying volume. The maximum bladder capacity during hydrodistension was lowered by 42.01% (p <0.001). The level of IL-8 in group I was higher on average by 28.57% (p = 0.434) as compared with that in group II, IL-6 — by 13.46% (p = 0.638), TNFα — by 9.09% (p = 0.244) and IL-1β — by 4.13% (p = 0.859). The number of mast cells in patients of group I vs. group II was higher by 40.65% (p < 0.05). In group I, a marked relationship was found between count of mast cells and plasma cells (r = –0.555, p > 0.05), as well as between count of plasma cells and IL-6 level (r = –0.639, p < 0.05). In group II, a significant connection was found between count of mast cells and TNFα level (r = +0.562, p < 0.05). Patients with Hunner’s IC/BPS are characterized by severe inflammation, wherein mast cells are involved in induction. Determination of cytokines in urine can provide a non-invasive division of IC/BPS into ulcerative and non-ulcerative groups.