The paper presents the results of a study of the female urethra in cases of urethral pain syndrome (UPS) and inflammatory diseases of the lower urinary tract using cross-polarization optical coherence tomography (CP OCT). Urethral wall structure was studied in 86 patients; 233 CP OCT images were collected. A comparative qualitative analysis of three groups of CP OCT images — “norm", “Inflammation" and “UPS" — identified that despite the absence of a clear inflammatory factor in the patient's examination, the urethral tissues in UPS were in an altered state. The changes in the urethral wall with UPS and in cases of inflammation were similar. Using a point scale, three experts independently performed visual scoring of the CP OCT images. Three parameters: epithelial contrast, cavities and the minimum signal depth in the co-channel were evaluated. It was found that, individually, the parameters correlate only weakly with the diagnosis. Area under the receiver operating characteristic (ROC) curve was from 0.51 to 0.78. The joint use of a number of visual signs has a greater diagnostic value than the use of the criteria individually. Area under the ROC curve using the developed cumulative criterion reached up to 0.87–0.89. This study could form the basis of a scoring system for assessing the state of the urethral tract using CP OCT images in real time. The CP OCT method provides information on the state of urethral tissues that cannot be obtained with traditional cystoscopy.