Background: Down syndrome (DS) is the most common chromosomal aberration, but the characteristics of the brainstem component in this condition during childhood (from newborn to preteen stages) have not been clarified. Objective: To evaluate the morphological features of the brainstem in DS on magnetic resonance imaging (MRI). Materials and methods: MRIs for 32 children with DS (16 boys and girls each; age range, 0-11 years) without major brain insults, and 32 age-matched controls (16 boys and girls each) were retrospectively analyzed. Height, width, and area of the midbrain, pons, and medulla oblongata were measured on sagittal T1-weighted images; these were compared in children with DS and age-matched controls. The ratios of the brainstem to the size of the posterior fossa (BS/PF index) were calculated; these were also compared in the children with DS and the control group. Results: The width and area of the midbrain; height, width, area of the pons; and area of the medulla oblongata were significantly smaller in children with DS than in control children (P < 0.05); the area of the pons, particularly for the ventral part, showed the largest differences in the mean relative differences. The BS/PF indices of the height, width, and area of the pons were significantly smaller in children with DS than in the control group (P < 0.01). However, the BS/PF indices for the midbrain and the medulla oblongata did not differ between these two groups. Conclusions: Children with DS may have small brainstems, particularly in the pons; this may be a characteristic morphological feature of the brainstem on MRI in childhood including neonates. (C) 2016 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.