Introduction: Prader-Willi syndrome (PWS) is a multisystem genetic imprinting disorder mainly characterized by hyperphagia and childhood obesity. Extensive structural alterations are expected in PWS patients, and their influence on brain nuclei should be early and profound. To date, few studies have investigated brain nuclei in children with PWS, although functional and structural alterations of the cortex have been reported widely.Methods: In the current study, we used T1-weighted magnetic resonance imaging to investigate alterations in brain nuclei by three automated analysis methods: shape analysis to evaluate the shape of 14 cerebral nuclei (bilateral thalamus, caudate, putamen, globus pallidus, hippocampus, amygdala, and nucleus accumbens), automated segmentation methods integrated in Freesurfer 7.2.0 to investigate the volume of hypothalamic subregions, and region of interest-based analysis to investigate the volume of deep cerebellar nuclei (DCN). Twelve age- and sex-matched children with PWS, 18 obese children without PWS (OB) and 18 healthy controls participated in this study.Results: Compared with control and OB individuals, the PWS group exhibited significant atrophy in the bilateral thalamus, pallidum, hippocampus, amygdala, nucleus accumbens, right caudate, bilateral hypothalamus (left anterior-inferior, bilateral posterior, and bilateral tubular inferior subunits) and bilateral DCN (dentate, interposed, and fastigial nuclei), whereas no significant difference was found between the OB and control groups.Discussion: Based on our evidence, we suggested that alterations in brain nuclei influenced by imprinted genes were associated with clinical manifestations of PWS, such as eating disorders, cognitive disability and endocrine abnormalities, which were distinct from the neural mechanisms of obese children.