Hypotonia is one of the most frequent signs of neurological pathology in newborn infants.To determine, in a 12-year retrospective study, the relative frequency of neurological pathologies that can be accompanied by hypotonia during the neonatal period and to describe the neurological development after two years' follow-up.We conducted a systematic review of the newborn infants with hypotonia due to an identifiable cause who were admitted to the neonatal unit of the Hospital Sant Joan de Deu between January 1996 and December 2008. Information collected referred to family history, data related with the pregnancy and childbirth, clinical features and complementary tests. RESULTS. A total of 73 hypotonic newborn infants were identified, 21 (28.7%) of whom met eligibility criteria. The majority, 81% (n = 17), were classified as central hypotonias and the remaining 19% (n = 4) were graded as peripheral hypotonias. In the first group, 47% (n = 8) presented chromosomal disorders, 29.4% (n = 5) had metabolic diseases and 23.5% (n = 4) displayed malformations of the central nervous system.The central causes of hypotonia continue to be the most prevalent in the neonatal period and, within these, chromosomal disorders are the most frequent. Peripheral causes are less common and have a more severe prognosis. Advances in molecular genetics have allowed many neuromuscular diseases to be diagnosed both genetically and at the molecular level. The diversity and complexity of the pathologies justifies a multidisciplinary approach being taken to treat these newborn infants.