Background: A considerable amount of cholesterol is needed by human body for the maintenance of tissue and various bodily metabolisms. Cardiac disorders are major cause for morbidity and mortality in recent years. Cord blood lipoprotein is influenced by factors such as placental insufficiency, mode of delivery, and conditions affecting fetal growth. The present study was planned to analyze cord blood lipid profile, apolipoproteins, and atherogenic index in different gestational age and compare them gender wise. Methods: A cross-sectional study was conducted in the Department of Obstetrics and Gynaecology, Geetanjali Medical College and Hospital, Udaipur. The study group included 640 neonates, divided into two groups on the basis of gestational age into near-term neonates (34–37 weeks) and term neonates (>37 weeks). The cord blood samples were taken from placental side of umbilical cord at birth. The blood was tested to determine lipid profile, apolipoproteins, and atherogenic index. Results: The results showed total cholesterol, triglyceride, HDL-C, LDL-C, ApoA-1, and Apo B level higher in near-term neonates group than term neonates. TC, TG, HDL-C, VLDL-C, and apolipoprotein A-1 were negatively correlated but LDL-C and apolipoprotein B were positively correlated with gestational age. Conclusion: The study showed that the gestational age is associated with lipid parameters. Prematurity as a factor was associated with atherogenic index.