The development of neonatal surgery is an important task of health care system, because birth defects have been the 2nd most prevalent cause of infant mortality for many years. In order to improve the quality of care for neonates with surgical diseases we studied the main causes of neonatal deaths during the period from 1995 to 2014, on the basis of data from the Children's Surgery Department of Yakutsk. In 77% of cases, the causes of lethal outcomes in neonates with surgical pathology were conditionally preventable. We singled out the basic organizational problems, the solution of which led to a 3.5 times reduction in mortality of infants with surgical pathology during the second period of the study (2005-2014). The main organizational aspects of the regional model of improving medical care of infants with surgical pathology are: antenatal diagnosis of malformations and prenatal consultation with children's surgeon, competent and timely transportation of newborns from district hospitals, the centralization of aid at level 3 hospitals, the introduction of modern diagnostic and treatment algorithms, methods of minimally invasive endosurgery.