Glut1 deficiency syndrome (Glut1-DS) is a neurological and metabolic disorder caused by impaired transport of glucose across the blood brain barrier (BBB). Mutations on the SCL2A1 gene encoding the glucose transporter protein in the BBB cause the syndrome, which encompasses epilepsy, movement disorders, and mental delay. Such variability of symptoms presents an obstacle to early diagnosis. The patients seem to share some craniofacial features, and identification and quantification of these could help in prompt diagnosis and clinical management. We performed a three-dimensional morphometric analysis of the faces of 11 female Glut1-DS patients using a stereophotogrammetric system. Data were analyzed using both inter-landmark distances and Principal Component Analysis. Compared with data collected from age-, sex-, and ethnicity-matched control subjects, common and homogenous facial features were identified among patients, which were mainly located in the mandible and the eyes. Glut1-DS patients had a more anterior chin; their mandibular body was longer but the rami were shorter, with a reduced gonial angle; they had smaller and down-slanted eyes with a reduced intercanthal distance. This study highlights the importance of morphometric analysis for defining the facial anatomical characteristics of the syndrome better, potentially helping clinicians to diagnose Glut1-DS. Improved knowledge of the facial anatomy of these patients can provide insights into their facial and cerebral embryological development, perhaps further clarifying the molecular basis of the syndrome. Clin. Anat. 30:644-652, 2017. © 2017 Wiley Periodicals, Inc.