Background Our previous research has suggested that genes around D12S1056 in 12q13 may confer susceptibility to ventricular septal defect （VSD） in humans. The present study was to define the chromosome region assignment by transmission disequilibrium test （TDT）, and to identify the important candidate gene by family-based association study and haplotype analysis. Methods Surrounding D12S1056, ten microsatellite markers including D12S329, D12S305, D12S1662, D12S1056, D12S1293, D12S334, D12S102, D12S83, D12S1655 and D12S1691 were chosen, and TDT was performed in 62 nuclear family trios each consisting of an affected child and two healty parents. Subsequently, the GLI gene, a positional candidate gene that maps to the target region, was selected for further analysis. Three single nucleotide polymorphisms （SNPs）, G11888C, G11388A, and G11625T, were selected for family-based association study and haplotype analysis. Results VSD was significantly associated with all selected markers except D12S1691 [72.2 centi morgen （cM）] and D12S1700 （75.76 cM）. VSD was also significantly associated with G11888C （X^2 = 5.918, P = 0.015）, G11388A （X^2 = 8.067, P = 0.005）, and G11625T （X^2 = 11.842, P = 0.001）. Haplotype analysis showed a strong linkage disequilibrium between G11888C and G11388A （D＇=0.999）, but in significant （X^2 = 1.035, df = 2, P 〉 0.05）. Conclusions The susceptibility gene of VSD was mapped to 3.56 cM in 12q13 by TDT, and the GLI gene, an important candidate in the target region, was associated with VSD.
