Abbreviations & Acronyms APF = antiproliferative factor BPS/IC = bladder pain syndrome/interstitial cystitis BUC = bladder urothelial cells CRP = C-reactive protein EGF = epidermal growth factor GP51 = glycoprotein 51 HB-EGF = heparin binding growth factor-like growth factor IC = interstitial cystitis IL = interleukin MCP-1 = monocyte chemotactic protein-1 MIP-1β = macrophage inflammatory protein OAB = overactive bladder NGF = nerve growth factor NIDDK = National Institute of Diabetes, Digestive, and Kidney Diseases TNF-α = tumor necrosis factor-α ZO-1 = zonula occludens-1 Abstract: There is a lack of consensus on the pathophysiology of bladder pain syndrome/ interstitial cystitis. The chronic pain symptoms of bladder pain syndrome/interstitial cystitis refractory to local treatment could be a result of central nervous system sensitization and persisting abnormalities in the bladder wall, which activate the afferent sensory system. Evidence also shows that bladder pain syndrome/interstitial cystitis is a heterogeneous syndrome and that the two subtypes, the ulcerative (classic) and non-ulcerative types, represent different disease entities. There is a need for non-invasive markers for the differential diagnoses of the subtypes of bladder pain syndrome/interstitial cystitis, and between bladder pain syndrome/interstitial cystitis and bladder sensory disorders, such as hypersensitive bladder syndrome or overactive bladder. Bladder pain syndrome/interstitial cystitis, but not overactive bladder, involves an aberrant differentiation program in the bladder urothelium that leads to altered synthesis of several proteoglycans, cell adhesion and tight junction proteins, and bacterial defense molecules. These findings have led to the rationale for identifying urinary biomarkers to detect bladder pain syndrome/interstitial cystitis in patients with frequency urgency syndrome. Recently, the markers that have been the focus of the most research are antiproliferative factor, epidermal growth factor, heparin-binding epidermal growth factor, glycosaminoglycans and bladder nitric oxide. In addition, inflammatory proteins in the urine and serum play important roles in the pathogenesis of bladder pain syndrome/interstitial cystitis. The urinary proteome is an easily accessible source of biomarkers for differentiation between inflammatory bladder disorders. Analysis of multiple urinary proteins and serum cytokines could provide a diagnostic basis for bladder pain syndrome/interstitial cystitis, and could be a tool for the differential diagnosis of bladder pain syndrome/interstitial cystitis and other sensory bladder disorders.