Neonatal surgical emergencies are common causes of neonatal morbidity and mortality. The aim of the study was to access epidemiological, clinical and prognostic characteristics of newborns hospitalized for surgical emergencies. Material and Methods: We conducted a one-year prospective study from January 1 st , 2016 to December 31 st , 2016 in the neonatology service in the Pediatric Department of Gabriel Touré Teaching Hospital in Bamako, the capital city of Mali. All neonates from 0 to 28 days hospitalized for a surgical emergency were included. Results: One hundred and fourteen cases of surgical emergencies were recorded, i.e. 3% of hospitalizations. The average maternal age was 24 years old. Sex ratio was 1.1. The average consultation time was 7.5 days. In 55% of cases, newborns were premature. The antenatal diagnosis was made in 7 patients. Congenital malformation pathology accounted for 92.98% of ailments. Digestive diseases predominated with 72.9%. These were mainly omphalocele (17.5%), anorectal malformations (13.2%), and laparochisis (12.3%). Hirshprung's disease was found in two newborns (1.8%). Surgery was performed in 59 neonates (51.8%). The per and postoperative lethality was 55.26%. The overall case fatality rate was 49.1%. The most lethal pathology was laparoshisis (100%). Factors associated with mortality were maternal insctruction level (p = 0.00), vaginal delivery (p = 0.01), and laparoschisis (p = 0.000). Conclusion: A real policy by the health authorities to reduce mortality related to neonatal surgical pathologies is needed.