Coeliac disease is known to cause neurological problems, although these are not well recognised by healthcare professionals. In this prospective study of 100 newly-diagnosed patients with classical coeliac disease, we show 67% to have neurological symptoms, and 46% to have abnormal NAA/Cr values by MR Spectroscopy investigation. Further, we demonstrate how participants with positivity to transglutaminase 6, an auto-antibody suggested to be involved in neuro-pathology of gluten-related disorders, are more likely to suffer these. Finally, we present a volumetric analysis showing subcortical atrophy in this sub-group. This study highlights the prevalence, and potential mechanisms, of neurological involvement in coeliac disease.