Introduction: Adiponectin has important anti-inflammatory and anti-atherogenic effects. Although adiponectin and atherosclerosis correlate inversely in children and adults, we have little information regarding this relationship in neonates. Methods: We measured cord blood adiponectin levels and abdominal aortic intima media thickness (aIMT) in 80 healthy, term neonates and investigated the relationship between adiponectin and total cholesterol (TC), LDL-cholesterol (LDL-C), HDL-cholesterol (HDL-C), and triglyceride, and their relationships to infant anthropometry and gender. Results: Mean birth weight, length, head circumference and aIMT values for male neonates were statistically significantly higher than those for female neonates. Adiponectin levels were not significantly different with respect to gender. In correlation analysis, the mean adiponectin level correlated positively with TC, HDL-C and LDL-C levels and birth weight, length and head circumference. There was no significant correlation between aIMT and any other parameters. Conclusion: The cord blood adiponectin and aIMT values reported here for the first time, represent reference values in the early neonatal period. The positive correlations between adiponectin levels and birth weight, length and head circumference, and TC, HDL-C and LDL-C indicate that further studies are required to demonstrate the exact relationship and clinical importance of adiponectin metabolism during the neonatal period.