This study on interstitial cystitis (IC) aims to identify unique urine metabolomic profile associated with IC, which can be defined as an unpleasant sensation including pain and discomfort related to the urinary bladder, without infection or other identifiable causes. Although the burden of IC on the American public is immense in both human and financial terms, there is no clear diagnostic test for IC, but rather it is a disease of exclusion. Very little is known about the clinically useful urinary biomarkers of IC, which are desperately needed. A comprehensive metabolomic profiling was performed using gas-chromatography/mass-spectrometry to compare urine specimens of IC patients (n=42) or health donors (n=19). Further study identified fifty-two IC-associated differentially expressed metabolites panel, including e rythronic acid, histidine, and tartaric acid et al. A clear stratification of IC patients from healthy controls was achieved (AUC 0.8968). Given that urine analyses have great potential to be adapted in clinical practice, this finding has the potential to be used as indicator for IC and to uncover important clues about underlying disease mechanisms.