To compare urinary nerve growth factor (NGF) and prostaglandin E2 (PGE2) levels among patients with detrusor overactivity (DO), increased bladder sensation (ISB), interstitial cystitis/bladder pain syndrome(IC/BPS) and controls. Urine samples were collected from 40 women with IC/BPS, 54 with overactive bladder (OAB) and 27 normal women as controls, all with a full bladder. Patients with OAB were further classified into subgroups of DO or IBS by urodynamic results. Urinary NGF and PGE2 levels were measured using an enzyme-linked immunosorbent assay. Urinary NGF and PGE2 levels were normalized by urinary creatinine (Cr) levels and compared among all subgroups. Urinary NGF levels were increased in the 40 women with IC/BPS and 23 with DO but not in 31 with IBS and the 27 controls. Mean (sd) urinary NGF/Cr levels were not significantly different between patients with IC/BPS, at 1.35 (0.36), and DO, at 1.93 (0.77). Urinary NGF/Cr levels were significantly higher in women with IC/BPS than in women with IBS, at 0.25 (0.10) (P=0.01). Using receiver operating characteristic curves for assessing urinary NGF/Cr levels in patients with IC/BPS and IBS, IC/BPS was diagnosed with a sensitivity and specificity of 75% and 65.5%, respectively, based on a urinary NGF/Cr threshold of 0.015. However, urinary PGE2/Cr levels were not significantly different among all subgroups. Urinary NGF/Cr levels are elevated in women with IC/BPS or DO, but not in those with IBS. The differential diagnosis of women with IC/BPS from those with frequency-urgency syndrome is possible based on urinary NGF/Cr levels but not urinary PGE2/Cr level.