This study aims to investigate the safety and clinical implication of intraperitoneal microdialysis (MD) in newborns operated on for congenital abdominal wall defect. 13 infants underwent intraperitoneal microdialysis (9 with gastroschisis and 4 with omphalocele). MD samples were collected every four hours and the concentrations of lactate, glycerol, glucose and pyruvate were measured. The results of MD were compared between the group of infants with gastroschisis and the group with omphalocele. The duration of parenteral nutrition and tube feeding were compared for high and low levels of intraperitoneal lactate, glycerol, and glucose and lactate/pyruvate ratio respectively. High and low levels were defined as above or below the median value on day one. Results from intraperitoneal MD showed a significantly higher mean lactate concentration in the group of infants with gastroschisis compared with the group of infants with omphalocele. The median values were 6.19 mmol/l and 2.19 mmol/l, respectively (P=0.006). The results from MD in the six infants in the gastroschisis group who underwent secondary closure after Silo treatment were similar to those who underwent primary closure. None of the infants with omphalocele received parenteral nutrition whereas all of the infants with gastroschisis did. There was no significant difference in duration of parenteral nutrition or tube feeding, respectively, when comparing the gastroschisis children with high versus low intraperitoneal lactate values. Placement of the MD catheter in the intraperitoneal cavity was feasible and without any major complications. Intraperitoneal MD is a safe procedure and an applicable method in surveillance of inflammatory changes in the peritoneal cavity in infants after operation for congenital abdominal wall defect. The true clinical value in infants with congenital wall defect remains unknown. Copyright © 2015 Elsevier Inc. All rights reserved.