To determine the association between polymorphism of UGT1A1 gene and idiopathic hyperbilirubinemia in Iranian neonates. Fifty neonates with idiopathic hyperbilirubinemia and Serum total bilirubin (STB) more that 15mg/dl and 50 neonates with idiopathic hyperbilirubinemia and Serum total bilirubin (STB) less than 15mg/dl enrolled in this study. Thymine-adenine (TA) repeats in the promoter region of UGT1A1 gene investigated by means of polymerase- chain reaction (PCR) DNA sequencing. Demographic characteristics did not differ significantly between groups while STB was higher in case group (17.5±1.9 vs. 10.4±1.8, p value<0.001). Among one hundred neonates evaluated in this study, TA6/6, TA6/7 and TA7/7 genotypes found in 52%, 42% and 6%, totally. TA6/7 and TA7/7 genotypes observed in case group more than the control group (P<0.001). STB levels were significantly higher in cases with TA6/7 and TA7/7 genotype pattern (P<0.001). Heterozygous and variant homozygous genotypes of the promoter region of UGT1A1 gene in healthy Iranian neonates with idiopathic hyperbilirubinemia should be considered.