Introduction: The goal of the study was to assess the course of painful syndrome in patients with bladder pain syndrome/interstitial cystitis and to assess the changes in endoscopic and histopathological findings in relation to the type of treatment. Patients and Methods: We included a total of 58 patients with histologically diagnosed interstitial cystitis. Out of these, 31 patients were treated with oral pharmacotherapy and 27 patients were treated by intravesical application of heparin. The patients were followed from time of diagnosis for 6.9 ± 2.5 and 6.6 ± 2.7 years, respectively. Results: Treatment – irrespective of its type – had a clear demonstrable effect on the monitored parameters; intravesical treatment was more effective than oral. Statistically significant (p < 0.05) changes could be observed in both groups (with two exceptions). When evaluating the relationship between subjective symptoms and objective criteria, and patients’ age and time to diagnosis, it is clear that the higher the age and the longer the time from symptoms to diagnosis, the more severe the symptoms. Conclusions: When evaluating the monitored parameters, we found significant correlations (both positive and negative). However, these relationships cannot be used to simplify the evaluation algorithm (according to ESSIC) and the initial criteria cannot predict the course of the disease.