INTRODUCTION There is a lack of knowledge on the average length of stay (LOS) in neonatal units after surgical repair of common congenital anomalies. There are few if any publications reporting the activity performed by units undertaking neonatal surgery. Such activity is important for contracting arrangements, commissioning specialist services and counselling parents. The aim of this study was to describe postnatal LOS for infants admitted to a single tertiary referral neonatal unit with congenital malformations requiring surgery. METHODS Data on nine conditions were collected prospectively for babies on the neonatal unit over a five-year period (2006)(2007)(2008)(2009)(2010)(2011). For those transferred back to their local unit following surgery, the local unit was contacted to determine the total LOS. Only those babies who had surgery during their first admission to our unit and who survived to discharge were included in the study. Cost estimates were based on the tariffs agreed for neonatal care between our trust and the London specialised commissioning group in 2011-2012. RESULTS The median LOS for the conditions studied was: gastroschisis 35 days (range: 19-154 days), oesophageal atresia 33 days (range: 9-133 days), congenital diaphragmatic hernia 28 days (range: 7-99 days), intestinal atresia 24 days (range: 6-168 days), Hirschsprung's disease 21 days (range: 15-36 days), sacrococcygeal teratoma 17 days (range: 12-55 days), myelomeningocoele 15.5 days (range: 8-24 days), anorectal malformation 15 days (range: 6-90 days) and exomphalos 12 days (range: 3-228 days). The total neonatal bed day costs for the median LOS ranged from £8,701 (myelomeningocoele) to £23,874 (gastroschisis). The cost of surgery was not included. CONCLUSIONS There is wide variation in LOS for the same conditions in a single neonatal unit. This can be explained by different types and severity within the same congenital anomalies, different surgeons and other clinical confounders (eg sepsis, surgical complications, associated anomalies). These data will enable us to give more detailed information to families following prenatal or postnatal diagnosis. They also allow more detailed planning of resource allocation for neonatal admissions.