Congenital heart defects (CHDs) are the most prevalent of all birth defects and the leading cause of death in the first year of life. The molecular causes of most CHDs remain largely unknown. The LIM homeodomain transcriptor factor ISL1 is a marker for undifferentiated cardiac progenitor cells that give rise to both the right ventricle and the inflow and outflow tracts, which are affected by several cardiovascular malformations. Contradictory findings about the role of the ISL1 rs1017 single-nucleotide polymorphism in increasing the risk of CHD have been reported. In this study, we aimed to investigate whether the ISL1 rs1017 genetic polymorphism conferred susceptibility to CHD in the white population. In a case-control study design, 309 patients with CHD (197 men [age 21.3 ± 25.2]) and 500 healthy controls (272 men [age 15.7 ± 21.3]) were genotyped for the ISL1 rs1017 polymorphism. No significant difference in the genotype and variant allele distributions was found between patients and controls. In addition, the ISL1 rs1017 polymorphism was not associated with the risk of CHD neither overall (p = 0.7) nor stratifying the population by sex and CHD classification. In conclusion, ISL1 common variant rs1017 is not associated with increased genetic risk of CHD in the white population.