Background Recent advances in renal replacement therapy (RRT) have brought about a proliferation of dialysis in neonates (<30 d). This study aimed to assess morbidity and mortality after RRT initiation in this population. Methods Retrospective chart review of all patients between 2006 and 2014 requiring RRT initiated in the first 30 d of life was performed. Results A total of 49 patients were identified, of which 39 were boys and 10 were girls. Thirty-two patients (65%) had end-stage renal disease, 11 (22%) had errors of metabolism, and six (12%) required RRT for other pathologies. Median age and weight at RRT onset were 6 (4-14) d and 3.1 (2.7-4.0) kg, respectively. A total of 201 surgeries were performed. Excluding catheter revisions, 83 new hemodialysis (HD) and 28 new peritoneal dialysis lines were placed, with maximum of six HD and four peritoneal catheters placed in single patient. Catheter-associated morbidities occurred in 100% of patients. Most common complications for HD included circuit clotting (87%), bleeding (68%), and bacteremia (50%). Peritoneal dialysis complications included peritonitis (83%), malpositioned catheters (72%), and leaks (55%). Overall mortality was 65.3%, with 56% of all deaths occurring within first month of life and 94% occurring within first year. Among long-term survivors (median follow-up of 5.3 y), 44% were severely and 22% moderately developmentally delayed. Conclusions Although RRT is becoming more technically feasible for neonates with renal and metabolic diseases, it remains associated with significant morbidity and mortality. Pediatric surgeons must be aware of the challenges, taking them into account when considering the care of these critically ill children.