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BACKGROUND: Fetal alcohol spectrum disorder (FASD) is a developmental disorder with severe negative lifetime consequences for the affected person. Numerous diagnostic methods for facial assessment in FAS exist, but most of them are based on subjective evaluations. Our aim was therefore to find objective methods for the verification of FAS(D). METHODS: 58 children (28 FAS; 30 controls) were examined prospectively. 3D facial scans were performed for each child and facial parameters at the mouth, nose and eye regions were measured and compared between the groups. RESULTS: Significant differences could be found for the distance between right and left sulcus nasi at the transition point to the philtrum (p < 0.001), for the inner canthal distance (p = 0.001) as well as for the right and left palpebral fissure length (p < 0.001). No significant difference between the FAS and control children could be found for the measurements of mouth breadth (p = 0.267) and breadth between the left and right alares nasi (p = 0.260). CONCLUSIONS: Measurements of mouth breadth and nose breadth for the alares nasi are not suitable for FAS diagnosis. In contrast, digital contactless measurements of the distance between the right and left sulcus nasi at the transition point to the philtrum, as well as the inner canthal distance and palpebral fissure length of the left and right eyes, showed significant differences when comparing children with FAS to healthy controls. These measurements could thus be additional objective means for the verification of FAS.