Congenital heart disease (CHDs) -whether it is associated with pulmonary hypertension (PH) or not- is the most common malformation in children. It is an important cause of infant mortality, long term morbidity and disability. Aim of the study is to assess the role of some genetic and environmental risk factors in patients with CHDs associated with PH. Subjects and methods: A case-control study was conducted and included 3 groups of cases; 37 patients with CHDs associated with PH, 37 patients with CHDs and 37 children without any congenital malformations were taken as a control group. The following clinical information was collected through predesigned questionnaires: maternal age at conception; parental consanguinity; maternal gestational diabetes (DM) and hypertension, adverse reproductive history (abortions and still births); and maternal environmental tobacco smoking (ETS) and deficient folic acid intake during pregnancy. Cytogenetic study for patients in the first and second groups of cases was carried out. Results: Chromosomal abnormalities were detected in 13.5% of patients with CHDs associated with PH and 10.8% of patients with CHDs. Maternal age, adverse reproductive history, maternal gestational DM and hypertension were not found to be significantly associated with congenital heart diseases in this study, while parental consanguinity, low maternal education level, maternal ETS and deficient folic acid intake during pregnancy were significantly associated with CHDs. Conclusion: It is crucial to make proper decisions and implement policies for lowering consanguineous marriages and provide proper pre-marital counseling and improving antenatal care to control the cases of CHDs.