Three single nucleotide polymorphisms (SNPs) associated with infantile hypertrophic pyloric stenosis have been identified by a genome-wide association study that included 1,001 surgically confirmed cases and 2,401 controls. Two of the SNPs are located in the vicinity of MBNL1, which encodes a factor important for splicing transitions that take place soon after birth. The other SNP is located downstream of NKX2-5, which has a role in the development of the embryonic gut and cardiac muscle tissue.