Neonatal “surgical” malformations are associated with higher costs than major “non-surgical” birth defects. We aimed to analyze the financial burden on the Austrian health system of five congenital malformations requiring timely postnatal surgery. The database of the Austrian National Public Health Institute for the period from 2002 to 2014 was reviewed. Diagnosis-related group (DRG) points assigned to hospital admissions containing five congenital malformations coded as principal diagnosis (esophageal atresia, duodenal atresia, congenital diaphragmatic hernia, gastroschisis, and omphalocele) were collected and compared to all hospitalizations for other reasons. Out of 3,518,625 total hospitalizations, there were 1664 admissions of patients with the selected malformations. The annual mean number was 128 (SD 17, range 110–175). The mean cost of the congenital malformations per hospital admission expressed in DRG points was 26,588 (range 0–465,772, SD 40,702) and was significantly higher compared to the other hospitalizations (n = 3,516,961; mean DRG 2194, range 0–834,997; SD 6161; p < 0.05). Surgical conditions requiring timely postnatal surgery place a significant financial burden on the healthcare system. The creation of a dedicated national register could allow for better planning of resource allocation, for improving the outcome of affected children, and for optimizing costs.