Neonatal hypotonia is a relatively common cause of consultation in daily pediatric practice. It is part of the clinical presentation of a large group of heterogeneous diseases, many of which have an important and classifiable genetic background. Identification of the specific disorder can help optimize the management and treatment of the patient and inform genetic counseling for the family, and therefore input from clinical geneticists is critical at the earliest stages of medical management. Here we present 30 patients with hypotonia of unknown etiology referred by a neuropediatrician to clinical genetics. Clinical, genetic, and molecular evaluation of each patient was performed. Sixty-nine percent of the patients included in the study had a genetic disease, including eight with Prader-Willi syndrome, three with spinal muscular atrophy, one with Rett syndrome, and one with Sotos syndrome harboring a previously undescribed mutation. Our data demonstrate that a multidisciplinary approach used from the outset that includes molecular analysis can help improve diagnosis and management of hypotonic infants. © 2014 Wiley Periodicals, Inc.