Congenital microphthalmia is a rare phenotype characterized by eye growth retardation. Due to the lack of eyeball stimulation, children suffering from congenital microphthalmia always have bony orbital maldevelopment, which leads to facial asymmetry. In the present study, a structured light 3D scanning system was used as a novel method to measure the three-dimensional periorbital asymmetry in children with congenital microphthalmia. Children with unilateral congenital microphthalmia of 0-6 years old were enrolled in the present study. All participants underwent an ultrasound scan to measure the axial length, and accepted the structured light 3D scanning system for their periorbital appearance. The degree of periorbital asymmetry was evaluated using 17 facial landmarks within a three-dimensional cartesian coordinate system (the X-axis represented the horizontal direction, the Y-axis represented the vertical direction, and the Z-axis represented the sagittal direction). Paired student t-test and ANOVA were used in the present study. A three-dimensional periorbital topography was also established to further illustrate the periorbital asymmetry. A total of 67 children were recruited, which included 31 boys and 34 girls. The axial length on the affected side (12.28 +/- 3.35 mm) was generally smaller than that on the unaffected side (20.54 +/- 1.65 mm, P < 0.001). When grouped by age, the periorbital asymmetry mainly manifested in the Y-axis and Z-axis directions. The unaffected side had a higher orbitale superior (5.09 +/- 0.35 vs. 3.02 +/- 0.30, P < 0.001) and a lower orbitale inferior (-19.52 +/- 0.51 vs. -16.90 +/- 0.53, P < 0.001) in 0-1 year old group. Same performances were also found in the 1-3 and 3-6 age groups. When grouped according to the proportion of axial length on the bilateral sides, seven of the 12 Y-values and all 12 Z-values had statistical differences. The structured Light 3D scanning system may serve as a beneficial complementary tool for computed tomography, in order to better understand the periorbital deformities caused by congenital microphthalmia. (C) 2021 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.