Prader-Willi syndrome (PWS) is a multiple-systemic disorder with many manifestations related to hypothalamic insufficiency, with obesity and behavioral problems as the major causes of morbidity and mortality. We describe a 2-day-old boy who initially presented with neonatal hypotonia and was diagnosed as PWS based on abnormal DNA methylation patterns in the small nuclear ribonucleoprotein polypeptide N (SNRPN) gene at the age of one week, despite the absence of other classical features. Molecular diagnosis for PWS, which has become available in recent years, should be considered for neonates with undiagnosed central hypotonia.