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Prolonged neonatal jaundice is usually benign but can occasionally indicate serious hepatobiliary disease. Current UK guidelines emphasise bilirubin-based screening, which may overlook atypical biochemical profiles. A term neonate presented with persistent jaundice but was otherwise well, with normal stools and urine. Bilirubin levels were normal, yet gamma-glutamyl transferase (GGT) was markedly elevated at 1101 U/L. Further testing revealed reduced alpha-1 antitrypsin (A1AT) levels and PiMZ heterozygosity. Imaging showed no structural abnormality. Over follow-up, transaminases—alanine aminotransferase and aspartate aminotransferase—rose, suggesting evolving hepatic involvement. Isolated GGT elevation, though uncommon, may represent the earliest clue to hepatobiliary disease. Heterozygous A1AT deficiency is not always benign and warrants ongoing biochemical surveillance. Clinicians should interpret guideline frameworks carefully to ensure atypical but clinically significant disease presentations are not overlooked.