Heme oxygenase-1 (HO-1) is a rate-limiting enzyme in bilirubin metabolism, and its genetic variant may modulate hyperbilirubinemia risk in neonates. The aim of the present study was to assess the association between heme oxygenase-1 gene variants and hyperbilirubinemia risk in Indian newborns. In a prospective case-control study, we analyzed (GT)n repeats and g.-413A>T variant of HO-1 gene and UGT1A1 gene variants in 100 case newborns with total serum bilirubin (TSB) levels exceeding 95th percentile and 100 control newborns with TSB levels below 75th percentile on the hour-specific bilirubin nomogram of the American Academy of Pediatrics. Study population consisted of term (37-41 weeks) and late preterm (34-36 weeks) newborns during the first 2 weeks of age. In our analysis, the (GT)n allele was highly polymorphic, ranging in number from 15 to 40. The incidence of short (GT)n allele (≤ 20) was significantly higher in neonates with hyperbilirubinemia than in controls. Although g.-413A>T variant was widely prevalent in the study population, no difference was noted in its prevalence between cases and controls. Short (GT)n repeats of HO-1 gene, c.211G>A variant of UGT1A1 gene, and excessive weight loss were independent risk factors for neonatal hyperbilirubinemia. In the presence of two or more risk factors, the odds of developing neonatal hyperbilirubinemia were high. Shorter (GT)n genotype in the promoter region of HO-1 gene is significantly associated with hyperbilirubinemia risk in Indian newborns. This genotype may interact with other genetic and clinical risk factors to further potentiate hyperbilirubinemia risk in newborns.