Aim Some inborn errors of metabolism induce metabolic encephalopathy through accumulation of neurotoxic metabolites. Rapid elimination of these metabolites by peritoneal or extracorporeal dialysis is crucial to prevent neuronal damage or death. In this retrospective study, we evaluated the outcomes of nine neonates with metabolic crisis treated with peritoneal dialysis. Method Six neonates with hyperammonemic coma (four with organic acidemias, two with urea cycle disorders) and three with leucine accumulation due to maple syrup urine disease (MSUD) were managed with peritoneal dialysis in conjunction with dietary and pharmacological therapy. Results Three patients with organic acidemia survived. One of the patients was normal; others had moderate and severe neurological impairments. One neonate with organic acidemia and both neonates with urea cycle disorders died. Two of the three patients with MSUD survived without neurological impairment; the other had severe neurological damage and died at 9 months of age due to sepsis. Conclusion Theoretically, extracorporeal dialysis should be the first dialysis treatment of choice; however, this report demonstrates that peritoneal dialysis has a chance to prevent neurological damage in some patients. Therefore, in developing countries without extracorporeal dialysis opportunities, it can be still a life-saving procedure, if it is applied with skilled staff and standard procedures. © 2014 The Authors. Journal of Paediatrics and Child Health © 2014 Paediatrics and Child Health Division (Royal Australasian College of Physicians).