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Background: Umbilical vein catheterization is a routine procedure in neonatal intensive care units. This invasive procedure, though easy and useful, can result in disastrous complications. Clinical Description: A 28 day old baby boy presented with umbilical sepsis along with multiple skin abscesses. He had a history of double volume exchange transfusion for Glucose 6 Phosphate deficiency induced hyperbilirubinemia, during the postnatal period. Ultrasound whole abdomen done to look for intra-abdominal abscesses revealed extensive portal vein thrombosis including the main portal vein and its branches with cavernoma formation. Upper gastrointestinal endoscopy revealed Grade II esophageal varices suggestive of the development of portal hypertension. Management and Outcome: Baby was started on subcutaneous enoxaparin which continued for 3 months. Follow up ultrasound showed complete obliteration of portal vein, replaced by cavernomas with development of grade II esophageal varices seen on upper gastrointestinal endoscopy. Conclusion: This case highlights how umbilical vein catheterization in the neonatal period can lead to catastrophic complications such as obliteration of the entire main portal vein and its branches, formation of portal cavernoma, portal hypertension, and esophageal varices, all of which can develop silently, at a very early age.