Abstract Background Interstitial cystitis/bladder pain syndrome is a bladder disease usually characterized by pain, urgency, and frequency. Interstitial cystitis is currently classified into two subtypes, with and without Hunner’s lesions. However, the underlying etiology of interstitial cystitis and its subtypes are largely unknown. Methods To better understand the biological changes in the bladder of interstitial cystitis/bladder pain syndrome patients, we directly analyzed bladder tissue of interstitial cystitis patients, both those with Hunner’s lesions and those without. Proteins in the bladder biopsies were analyzed using nanoscale high-performance liquid chromatography-tandem mass spectrometry. Disease subgroups were compared and significantly expressed proteins were mapped using STRING to determine protein associations and functions. Results We found that patients with Hunner’s lesions had significant increases in inflammatory and endoplasmic reticulum stress proteins, with a decrease in cellular adhesive proteins, compared to patients without Hunner’s lesions. These patients also exhibited a decrease in proteins associated with the Rap1 signaling pathway, which regulates cell proliferation and wound healing. When comparing diseased and non-disease-apparent tissue in patients with Hunner’s lesions, diseased tissue exhibited a decrease in ubiquitination proteins. Conclusions In summary, there are significant differences in protein expression found in the bladders of interstitial cystitis patients with and without Hunner’s lesions, indicating a disturbance in proteins associated with cellular adhesion, proliferation, protein processing, and wound healing.