Background: There are many studies about the association of nephropathy with congenital heart diseases (CHD), and the risk factors such as cyanosis and pulmonary hypertension have been evaluated. In our study, we have considered the relation of CHD associated nephropathy with other newer factors and the type of the structural heart defect. Materials and Methods: A prospective cross sectional study was carried out. 48 children were selected on the basis of specific inclusion criteria, and reviewed over a period of 9 months. Nine different simple and complex structural heart defects were evaluated and compared after obtaining the imaging, blood and urine test results. Results: Significant proteinuria occurred in 8 patients included in the study. More severe forms of pulmonary hypertension were observed in patients suffering from truncus arteriosus (TA); while the least values were detected in cases of pulmonary stenosis (PS) and tetralogy of fallot (TOF). The highest values of protein excretion were seen in patients of TA; and, the lowest values were observed in patients of PS and aortic stenosis (AS). Renal insufficiency was uncommon in infants and children with CHD. Conclusion: TA is an important cause of proteinuria among the infants and children suffering from CHD, probably because of the associated severe pulmonary hypertension (PH) and cyanosis. Also, proteinuria occurred at an earlier age in patients of TA as compared to other conditions, and was also found to be more severe if the TA was associated with moderate to severe tricuspid regurgitation.