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Objectives Histological studies have shown alterations of thalamic nuclei in patients with Down syndrome (DS). The correlation of these changes on MRI (magnetic resonance imaging) is unclear. Therefore, this study investigates volumetric differences of thalamic nuclei in children with DS compared to controls. Methods Patients were retrospectively identified between 01/2000 and 10/2021. Patient inclusion criteria were: (1) 0–18 years of age, (2) diagnosis of DS, and (3) availability of a brain MRI without parenchymal injury and a non-motion-degraded volumetric T1-weighted sequence. Whole thalamus and thalamic nuclei ( n = 25) volumes were analyzed bilaterally relative to the total brain volume (TBV). Two-sided t-tests were used to evaluate differences between groups. Differences were considered significant if the adjusted p-value was <0.05 after correction for multiple hypothesis testing using the Holm-Bonferroni method. Results 21 children with DS (11 females, 52.4%, mean age: 8.6 ± 4.3 years) and 63 age- and sex-matched controls (32 females, 50.8%, 8.6 ± 4.3 years) were studied using automated volumetric segmentation. Significantly smaller ratios were found for nine thalamic nuclei and the whole thalamus on the right and five thalamic nuclei on the left. TBV was significantly smaller in patients with DS ( p < 0.001). No significant differences were found between the groups for age and sex. Conclusions In this exploratory volumetric analysis of the thalamus and thalamic nuclei, we observed statistically significant volumetric changes in children with DS. Our findings confirm prior neuroimaging and histological studies and extend the range of involved thalamic nuclei in pediatric DS.