A full-term male neonate from a first pregnancy of two clinical non-consanguineous parents was born at 40 weeks of gestation with cesarean section. He was admitted at 2 hours of life to our III level Neonatal Intensive Care Unit due to generalized hypotonia, presenting at birth. Cerebral ultrasound showed a temporal bilateral aspecific alteration of the parenchimal echogenicity, whereas a magnetic resonance imaging/venography revealed an extensive cerebral sinus thrombus. Extensive diagnostic studies for prothrombotic disorders showed negative results, even if there was an alterated haemostatic screening. Persistency of hypotonia led us to investigate Prader-Willi syndrome among others. Methylation analysis confirmed the diagnosis. This is the third report associating cerebral venous thrombosis and Prader-Willi syndrome, confirming sinus thrombosis as a possible presentation of this syndrome. A review of the literature is provided in order to disclose possible similarities and differences in Prader-Willi syndrome patients with cerebral sinovenus thrombosis.