Potential celiac disease (CeD) patients have immunological abnormalities similar to CeD but unlike CeD, their duodenum displays normal histology. In-vitro proton NMR study of small intestinal mucosa of these patients demonstrated metabolic abnormalities associated with the intestinal inflammation. Both potential CeD and CeD patients had lower concentration of histidine compared to controls while lower glycine was seen only in CeD. Since, both amino acids exert anti-inflammatory effects; their reduced levels suggested compromised cytoprotective mechanism. Significantly higher level of glycerophosphocholine seen in potential CeD compared to CeD might have contributed for renewal of enterocytes and thus to normal small intestine histology.