Objectives: Neonates with major gastrointestinal surgical conditions frequently suffer from prolonged feed intolerance, infections, and need multiple courses of antibiotics. All these put them at risk of gut dysbiosis. Probiotic supplementation has the potential to minimise dysbiosis and improve clinical outcomes in such infants. Hence, we aimed to conduct a systematic review of probiotics in neonates with major surgical conditions of the gut. Methods: Medline, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), and other databases were searched in September 2016. Results: Two randomised controlled trials (RCTs) were included; the first was conducted in 24 neonates with gastroschisis, the second in eight neonates with various surgical conditions. In the first study, the overall microbial communities were not significantly different between groups, though analysis of the final specimens demonstrated higher Bifidobacteriaceae, lower Clostridiaceae, and trends toward lower Enterobacteriaceae, Enterococcaceae, Staphylococcaceae, and Streptococcaceae in the probiotic group. In the second study, there were significantly more Streptcoccaceae in the faecal samples in the probiotic group and significantly more Bifidobacteriaceae in the no probiotic group (p <.05). Conclusions: There is limited evidence regarding the role of probiotics in neonates with gastrointestinal surgical conditions. Adequately powered RCTs are needed to address this issue.