Purpose <p>Prader-Willi Syndrome (PWS) is a rare genetic disorder with a heterogeneous phenotype, caused by loss of expression of genes on the paternally inherited chromosome 15q11.2-15q13.3, primarily due to paternal deletion of these genes. PWS with paternal deletion can be categorised into sub-genotype 1 (PWS T1) and sub-genotype 2 (PWS T2), with PWS T1 encompassing a more extensive genetic deletion with distinct clinical manifestations. Neuroimaging studies have shown structural alterations in the hypothalamus and other brain structures of PWS patients, but no distinctions were made between PWS sub-genotypes in patients with a paternal deletion. This study aimed to differentiate between PWS T1 and T2, exploring volumetric differences of the hypothalamus and other brain structures using T1-weighted MRI.</p> Methods <p>Structural T1-weighted MRI images from 6 PWS T1 patients, 6 PWS T2 patients, and 13 controls underwent pre-processing and segmentation. Brain structure volumes were normalised for intracranial volume using the residual method. Right-sided hypothalamic data were excluded due to unreliable segmentation outcomes.</p> Results <p>Total intracranial volume was significantly smaller in PWS patients compared to controls. After adjustment, the left-sided hypothalamus and hypothalamic subunit volumes were smaller in the PWS group. Lateral ventricle, third ventricle, cerebrospinal fluid and total ventricle &amp; choroid plexus volume were significantly larger in the PWS group compared to the control group, whereas mid-posterior corpus callosum volume was smaller. Cerebellar volume was smaller in PWS T2 patients compared to PWS T1 patients.</p> Conclusion <p>Future research should further distinguish PWS sub-genotypes to enhance personalised medicine for PWS patients.</p>