The practise of evidence based medicine means integrating the clinical expertise with the best available external clinical evidence from systematic research. There is a lack of supporting scientific evidence from rigorous trials in neonatal surgery. The indications for surgery and the type of operation performed in neonates are rarely supported by randomised controlled trials. As a consequence, the majority of the operations performed in neonates are supported by retrospective studies and surgeon preference. This review article is focussed on operations in neonates which are performed by general paediatric surgeons. Only a few randomised controlled trials have been performed in neonatal diseases such as congenital diaphragmatic hernia, necrotizing enterocolitis, pyloric stenosis and inguinal hernia. All of these trials have been based on collaboration between paediatric surgical units highlighting the importance of creating a network of centres that will promote multicentre prospective studies.