We report the anaesthetic management of a 3-year-old-child with microvillus inclusion disease undergoing isolated small bowel transplantation. He required long-term total parenteral nutrition which was complicated with numerous episodes of catheter related sepsis. This resulted in thrombosis of the major blood vessels which critically restricted vascular access available for intravenous nutrition, becoming a life-threatening condition for the patient. Haemodynamic, respiratory parameters and urinary output were well preserved throughout the procedure. Besides a transitory increase in potassium following graft revascularization, biochemical changes were small. Anaesthetic management included comprehensive preoperative assessment, central venous angiography to depict accessibility of central and peripheral veins, assurance of additional vascular access through the intraoperative catheterization of the left renal vein, perioperative epidural analgesia and preservation of splanchnic perfusion to ensure implant viability.