Objective: Fetus with intrauterine stress may exhibit programmed changes that can alter its metabolism and bear severe risk for diseases in adult life. The current study was designed to assess the correlation between cord blood lipid profile with the anthropometric data in neonates. Materials and methods: 146 newborn babies born at Dr. T M A Pai Hospital, Udupi were screened and their birth weight, length, head circumference and abdominal circumference were noted at birth. Umbilical cord blood samples were analyzed for total cholesterol, triglycerides (TG), high density lipoprotein (HDL) and low density lipoprotein (LDL). Infants were also grouped further based on gestational age (GA) and sex-adjusted birth weight percentiles into three groups i.e. Small for gestational age (SGA), Appropriate for gestational age (AGA) and Large for gestational age (LGA) for comparison of their lipid profiles. Inclusion criteria were normal fetal heart rate at birth and an APGAR score [7. Statistical significance of relation between lipid profile and anthropometry was done using ANOVA and Pearson correlation coefficient. Results: Triglycerides were significantly higher in babies with higher ponderal index (PI) than those with lower PI (P = 0.011). The TG level of SGA babies were significantly higher as compared to AGA group (P = 0.001). The LDL levels in neonates with higher abdominal circumference were significantly lower than those with lower AC (P = 0.019). Mean HDL levels were higher in neonates with larger AC, but not statistically significant. Maternal BMI had no influence on neonates' lipid profile. Conclusion: Abnormal intrauterine milieu created by maternal changes during gestation may bear a profound impact on lipid metabolism in neonates, which may account for their differences in lipid profile and anthropometry at birth.