The aim of this study was to explore genetic mechanisms of congenital heart disease by analysing family data. Families with two or more affected members were studied, and information on family history and risk factors was collected. A total of 25 families with congenital heart disease were identified, and among them the condition was confirmed in 57. The prevalence of congenital heart disease in first-degree relatives was 43.0%, that is 46 out of 107, significantly higher than that in second-degree relatives, that is, 4.4%, 11 out of 252) (χ2 = 83.897, P < 0.01). The prevalence difference between twins (90%) and siblings (62.2%) (χ2 = 4.983, P < 0.05) was also significant among first-degree relatives. Eleven families were found to have the same phenotype (44%), including ventricular septal defect in six families, atrial septal defect in two families, conotruncal defects in two families, and hypoplastic left heart syndrome in one family. Both twins were diagnosed with congenital heart disease in 8 out of 10 twin families – all eight twins were monozygotic. The cardiac phenotype of the twins was consistent in three families (37.5%). The cardiac phenotype of first- and second-degree relatives was not fully consistent with their probands. There was an increased incidence of threatened abortion in early pregnancy in patients with familial congenital heart disease when compared with sporadic congenital heart disease (χ2 = 8.704, P < 0.05). Morbidity in relatives was related to blood relationship, with a closer relationship increasing the risk of congenital heart disease. Genetic factors appear to play an important role in congenital heart disease.