Coeliac disease (CD) is a well defined condition contributed to by both genetic and environmental factors. The clinical management of CD is becoming increasingly complex as the disparity between symptoms, biological markers and mucosal pathology becomes more apparent. The only available treatment for CD is a life-long strict gluten-free diet (GFD), but up to 86 of adult patients fail to achieve complete mucosal recovery even after 2 years of a GFD. The only accurate means of monitoring recovery on a GFD is via histology, which is cumbersome and resource intensive. Therefore, there is a need for novel non-invasive techniques for diagnosis and monitoring that are more accurate than serum antibodies in addition to an improved understanding of the disease mechanisms and obstacles to recovery. Metabolomics may address these needs. Metabolomics can be used to evaluate biomarkers associated with human disease from a variety of biological matrices including blood, urine and tissue samples. Through the comprehensive analysis of metabolites, metabolomics offers great promise for the early detection of CD and convenient monitoring of response to a GFD and perhaps an accurate means of assessing compliance to a GFD. As more evidence of the importance of gut microflora in human health accumulates, metabolomics may also be applied to investigate microbiome-metabolome interactions in CD for the most comprehensive understanding of this disease to date.