Introduction: The mortality rate due to omphalocele cases remains high. The presence of other congenital anomalies is believed to be one of the factors causing death in patients with omphalocele. The objective of the study was to determine the influence of other congenital anomalies leading to mortality. Methods: We conducted a retrospective cohort study in the neonatal unit of Sardjito General Hospital from March 2008-April 2019. We collected data on factors including sex, mode of delivery, gestational age, birth weight, associated anomalies, management, neonatal complications, need for surgeries, and mortality from our registry and patients’ medical records. We then classified the infants into the isolated omphalocele and non-isolated omphalocele groups. Univariate and multivariate analyses were performed to determine the association of congenital anomalies and other confounding factors with mortality. Results: We identified 73 omphalocele cases during the study period. The hospital occurrence was 4.3/1000 livebirths. We found 45 cases (61.6%) of omphalocele associated with other congenital anomalies including several syndromes (46.7%) such as Patau syndrome and Beckwith-Wiedemann syndrome, congenital heart defects (42.2%), gastrointestinal anomalies (22.2%), neural tube defects (15.6%), cleft palate (11.1%), and syndactyly (0.07%). There was no difference in mortality (25/45 vs 15/28) between the groups (p=0.87). Interestingly, sepsis, pneumonia and gastrointestinal perforation were significantly associated with the survival of infants with omphalocele, with p-value of 0.05, 0.00, and 0.05, respectively. Conclusion: Certain complications might have an impact on survival, but the presence of other congenital anomalies was not significantly associated with the mortality of omphalocele cases.