Congenital heart disease (CHD) is the most common birth abnormality, but the etiology of CHD is unknown. ISL1 may play a fundamental role in cardiac morphogenesis, and mutations of this gene could cause CHD. To evaluate whether genetic variations of ISL1 are associated with CHD in Chinese Han people, polymerase chain reaction restriction fragment-length polymorphism and SNaPshot were used to examine 9 polymorphisms of ISL1 in 233 patients with CHD as well as 288 healthy controls. We found that one SNP (rs1017) in ISL1 was significantly associated with simple CHD. Genetic variation of ISL1 was confirmed to be associated with the risk of CHD. ISL1 is related to the atrial septal defect group and the ventricular septal defect group, and the genotypes were associated with the occurrence of CHD in the dominant mode of inheritance. We concluded that rs1017 contributed to the risk of CHD in Chinese Han people, and ISL1 may be involved in the formation and development of the heart.