The diagnosis of gastrointestinal (GI) disorders is usually based on invasive techniques such as endoscopy. A key important factor in GI cancer is early diagnosis which warrants development of non-or lessinvasive diagnostic techniques. In addition, monitoring and surveillance are other important parts in the management of GI diseases. Metabolomics studies with nuclear magnetic resonance and mass spectrometry can measure the concentration of more than 3000 chemical compounds in the urine providing possible chemical signature in different diseases and during health. In this review, we discuss the urinary metabolomics signature of different GI diseases including GI cancer and elaborate on how these biomarkers could be used for the classification, early diagnosis and the monitoring of the patients. Moreover, we discuss future directions of this still evolving field of research. Core tip: Scientists are always searching for new disease biomarkers. An acceptable biomarker could help us in early diagnosis and classification of the diseases as well as the prediction of disease outcome. The diagnosis of gastrointestinal (GI) diseases is usually based on techniques such as upper or lower GI endoscopy, while highly sensitive and specific non-invasive diagnostic or screening tools are usually lacking. In this review, we have discussed the potentials of urinary metabolomics study as a future tool for the screening, diagnosis, classification and surveillance of GI diseases including inflammatory bowel disease and cancer.