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Apert syndrome is characterized by the severe craniofacial deformities. The subsequent process of skeletal maldevelopment is likely to be influenced by multiple interactions at several levels, at a given time. In this study, we aimed to explore the evolution of cranial basal dysmorphology and the chronology of these deformities in Apert syndrome, by objectively analyzing three-dimensional measurements. Fifty-four CT scans from unoperated patients (Apert, n = 18; control, n = 36) were included in this study, with age range from 3 days to 24 years. Before 6 months of age, Apert's anterior cranial base was widened 60%. Between 6 months and 2 years of age, the whole cranial base length, anterior cranial base length and posterior cranial base length decreased 8%, 8% and 14%, respectively. The greater sphenoid wing angle was wider by 26.0°, and continued into adulthood. The cranial base angles did not produce significant changes throughout life. The extra cranial distances synchronously and almost proportionally shortened after later infancy. The anterior and posterior cranial base length shortened at an almost proportional rate. The malformations of the skull vault are additive effects with cranial base fusion on skull length restriction, but the angulation of the skull base is virtually normal., (Copyright © 2018 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)