Celiac Disease (CeD) is a systemic autoimmune enteropathy in which intolerance to gluten leads to villous atrophy through an inflammatory cascade. The diagnosis of CeD is challenging due to wide variation in clinical manifestations. Although histological features in CeD are characteristic, they are not specific. Metabonomics studies may help in characterizing new biomarkers for the diagnosis and prognostic value in CeD. The objectives of this study were (i) to evaluate the biochemical profile of the urine from CeD patients and healthy controls (HC) using NMR spectroscopy at 700 MHz, and (ii) to quantify the various metabolites observed in NMR spectra and identify the possible biochemical markers for CeD that would aid in the diagnosis. Thirty patients with CeD (n=30; mean age 25.5 ± 10.5 yrs) and fifteen healthy controls (n=15; mean age 28.9 ± 5.5 yrs) were recruited. Informed consent was obtained from all subjects and Institute Ethics Committee approved the study. European Society of Pediatric Gastroenterology Hepatology and Nutrition criteria was used for diagnosis of CeD. CeD patients exhibited significantly higher urinary excretion of β-hydroxybutyrate, pyruvate and allantoin as compared to HC. High level of ketone bodies like β-hydroxybutyrate indicates inefficient utilization of glucose. Further, pyruvate is produced by the anaerobic breakdown of glucose and its higher concentration may reflect modulation in energy metabolism. Elevation in the concentration of allantoin may be the consequence of inflammatory processes observed in CeD. In addition, significant decrease was observed in the concentration of citrate and creatinine in urine sample of CeD patients. The chronic diarrhea associated with CeD may lead to decreased urinary excretion of citrate while lower creatinine is indicative of protein malabsorption in CeD patients. Our results demonstrated potential utility of NMR based metabonomics in understanding the metabolic alterations and in characterization of biomarker/s for diagnosis of CeD.