Clinically apparent jaundice is unusual in patients with beta-thalassemia major. Co-inheritance of Gilbert syndrome has been reported to cause hyperbilirubinemia in these subjects. Crigler-Najjar syndrome is another rare disorder of bilirubin metabolism caused by mutation in the gene coding the enzyme UGT1A1. We report a patient of beta-thalassemia major who presented with persistent jaundice due to co-inherited Crigler-Najjar syndrome type 2 secondary to a novel mutation in UGT1A1 gene [homozygous base substitution at position 362 (GGT>AGT) in exon 3].