Given the widespread problems of obesity and diabetes both in Puerto Rico and in the United States as a whole, there is an urgent need to investigate the complex interaction between BMI, pre-gestational and gestational maternal diabetes, and its possible impact on the occurrence of congenital heart defects (CHD) during neonatal development. Using the Comprehensive Congenital Defects Surveillance System in Puerto Rico, we performed a focused analysis on newborns diagnosed with CHD between 2016 and 2020. Our evaluation covered a variety of variables, including maternal age, gestational age, BMI, pre-gestational diabetes, gestational diabetes, hypertension, history of abortion, and the presence of preeclampsia. A cohort of 673 patients was included in the study. The average maternal age was 26 years, with a range of 22 to 32 years. The average gestational age was 39 weeks, with a mean range of 38 to 39 weeks. Of the 673 patients, 274 (41%) mothers gave birth to newborns diagnosed with CHD. Within this group, 22 cases were linked to pre-gestational diabetes, while 202 were not; 20 cases were associated with gestational diabetes, compared to 200 without this condition; and 148 cases had an overweight or obese BMI, while 126 showed a normal BMI.