Background Searching biomarkers of irritable bowel syndrome (IBS) is emerging topic. Previous studies searched limited biomarkers and largely ignored real exacerbation of IBS symptoms in patient's life. We hypothesized that we can identify biomarkers of IBS which are associated with changes in IBS symptoms using urinary metabolomics.Methods Subjects were 25 IBS patients (33.0 ± 2.1 y.o., 15 male, 10 female) diagnosed with Rome III criteria (12 with diarrhea, 11 mixed, and 2 with constipation) and ageand sexmatched healthy controls. Subjects completed ordinate scales containing abdominal pain and discomfort everyday for 28 days. Simultaneously urinary samples were collected at the first day, the day with exacerbation, and the 28th day with questionnaires including IBS Severity Index (IBS-SI) and IBS Quality of Life (IBS-QOL). Urinary samples were immediately frozen, stored, and later analyzed with ultraperformance liquid chromatography and mass spectrometry. After correction with creatinine, data were analyzed statistically with generalized estimating equation (GEE) using SPSS ver. 21.0 followed by multiple regression analysis with IBS symptoms as dependent variables and metabolites as independent variables. Results We first identified 191 metabolome markers. GEE revealed significant 44 markers with group (IBS vs controls) effect and/or time effect and/or group time interaction. IBS patients showed significantly lower kynurenic acid (p < 0.005), xanthurenic acid (p < 0.001), homovanillic acid (p < 0.005), vanillylmandelic acid (p < 0.005) and glycylglycine (p < 0.001) than controls. IBS patients showed significantly higher quinolinic acid (p < 0.01), 3-methoxytyamine (p < 0.05), xylose (p < 0.005), 2'-deoxyguanosine (p < 0.001), 2'-deoxyadenosine (p < 0.05), and N-acetylarginine (p < 0.05) than controls. Multiple regression analysis disclosed xylose as significant predictor of abdominal pain (R2 = 0.859, b = 0.59, p < 0.0001). Conclusion These findings support our hypothesis and suggest that increased urinary xylose level reflects increased mucosal permeability in IBS patients. Moreover, increased quinolinic acid and decreased kynurenic and xanthurenic acids in IBS patients may cause toxicity of the glutamatergic neurons expressing NMDA receptors both in the brain and the gut.