The risk allele [T] of HAAO rs3816183 had an association with increased risk of middle (OR = 2.130, 95% CI = 1.072–4.232, p=0.028) and anterior/middle (OR = 1.775, 95% CI = 1.005–3.135, p=0.046) hypospadias. This evidence concerns the gene HAAO and hypospadias.