Background: Surgery on a newborn has been one of the most challenging subjects in medical science. A neonate is born with its unique physiological features of very narrow normal ranges, beyond which it is helpless to cope with the adverse situations. Added to this, it has to be able to respond to life-threatening surgical conditions for its survival. Objectives: We aimed in this piece of work to assess the outcome of different neonatal surgical conditions and factors responsible for mortality in surgical neonates. Patients and Methods: The present retrospective study was conducted in the NICU of Ain Shams University Children’s Hospital using the records from the beginning of year 2011 till the end of year 2013. The recorded data included gestational age, postnatal age at admission, sex of neonates, maternal age, mode of delivery, surgical diagnosis, surgery outcome, risk factors for occurrence of sepsis, classification of type of sepsis if present (Early-onset sepsis, Late-onset, or nosocomial) , blood culture results, antimicrobials used, length of hospital stay, need for ventilation, risk factors for occurrence of sepsis, cause of death. Results: The study included 69 patients with surgical problems who were admitted to the NICU. They were 45 males (65.22%) and 24 females (34.78%) with a male to female ratio of 1.8: 1. They were 10 preterms (14.49%) and 59 full-terms (85.51%); with mean gestational age range from 32-40 weeks, mean ± SD: 36.91±1.98 weeks. 37 (53.62%) were delivered by LSCS and 32 (46.38%) by SVD. 33.33% of neonates were admitted between 1 and 2 days postnatal, 42.9% were more than 1 week old, with mean age of admission 9.49 ±10.37 days. The most common surgical problems were Tracheo-oesophageal fistula (9 cases), followed by imperforate anus low anomaly 5 cases, imperforate anus high anomaly 5 cases, then Hirshsprung disease 4 cases. Also hydrocephalus and Arnold Chiari malformation each 4 cases. Diaphragmatic hernia 4 cases. 61 cases had sepsis, 50 cases were discharged, 19 died and 8 had no complications. The most common causes of death were; sepsis (16 cases), heart failure (9 cases), respiratory failure (5 cases), cardio –pulmonary failure (3 cases) and pneumonia and pulmonary hypertension each one case. Conclusion: Most of cases were full term babies and had late presentation to our hospital which led to delayed operations. Most common surgical problem was trachea-oesophageal fistula.