Hypospadias is a common congenital malformation of the male external genitalia. Most cases have an unknown etiology, which is probably a mix of monogenic and multifactorial forms, implicating both genetic and environmental factors. Ryanodine receptor 1 () mutations are a common cause of congenital diseases associated with both dominant and recessive inheritance in humans. Herein, we evaluated the correlations of C6487T polymorphism with the risk and severity of hypospadias.263 congenital hypospadias children and 312 healthy children were recruited. The polymorphism of C6487T in the peripheral blood was detected by polymerase chain reaction-restriction fragment length polymorphism, and different genotypes and allelic genes were analyzed to explore their associations with the risk of congenital hypospadias.The distribution frequencies of CC/CT/TT genotypes and two alleles (C and T) at C6487T showed significant differences between the case and control groups ( < 0.05). The frequency of C allele in the case and control groups was 46.95% and 54.94%, respectively, and of T allele was 53.05% and 45.06% ( < 0.05). In addition, the distribution frequency of CC/CT/TT genotypes exhibited significant difference between patients with mild hypospadias and those with moderate or severe hypospadias (all > 0.05), suggesting that C6487T polymorphism is correlated with the severity of congenital hypospadias (X = 13.722, = 0.001).Our study demonstrated that C6487T polymorphism might be associated with an increased risk of congenital hypospadias in Chinese Han children. Our findings highlight the heterogeneous nature of hypospadias genetic susceptibility.