Facial dysmorphology is an important feature in several lysosomal storage disorders. Although in Fabry disease facial dysmorphism is not a prominent sign, minor facial abnormalities have been previously reported. By analysing three-dimensional images of faces, we quantified facial dysmorphology in a cohort of both male and female Fabry patients. Morphometric analysis of different regions of the face revealed significant differences in face shape in male patients and to a lesser extent in female patients. In male patients, the most prominent abnormalities were located in the peri-orbital region. Pattern recognition techniques achieved a discrimination accuracy of up to 85% for male patients compared with healthy controls. The discrimination accuracy in female patients achieved only 67%. This objective method for facial dysmorphology assessment provided evidence for significant differences in face shape in both male and female Fabry patients compared with controls. However, because discrimination from healthy controls is too low, no key role in the diagnostic process can be expected.