Background: One of the most potent and consistently suggested risk factors for congenital heart disease (CHD) in the newborn is maternal diabetes. Diabetes is prevalent and increasing in Iraq, and babies born to diabetic mothers (IDM) are a large, identifiable, and screenable high-risk group. Objectives: To estimate the rate of CHD in infants of diabetic women as compared to infants of non-diabetic women, describe the pattern of defects, and identify maternal risk factors. Methods: The prospective hospital-based cohort with a non-diabetic control group was conducted in a maternity and children's hospital in Najaf. Within their first week of life, 300 neonates of diabetic mothers underwent transthoracic echocardiography, as did 300 neonates of non-diabetic mothers. The risk ratios and multivariable logistic regression were used. Results: CHD was found in 11.7% of IDMs versus 2.7% of controls (relative risk ≈ 4.4; 95% CI 2.1–9.3; p < 0.001). Ventricular septal defect (31.4%), atrial septal defect (22.9%), patent ductus arteriosus (20.0%), and hypertrophic cardiomyopathy (14.3%) were the most common defects observed in IDMs. For diabetic women and pregestational diabetes (failure to achieve good glycemic control in the first trimester (HbA1c >7%) was found to be an independent risk factor for CHD. Conclusion: Diabetic mothers' infants have approximately four times the risk of CHD, the majority of which has been attributed to pregestational diabetes and poor periconceptional glucose control. This report suggests the need for preconception counseling, strict glycemic regulation in the first trimester, and the routine fetal/neonatal echocardiographic screening of diabetic pregnancies in Iraq.