Objective To identify the role of longitudinal measurements of fetal aortic isthmus blood flow using Doppler ultrasonography in the prediction of perinatal morbidity and mortality. Setting Obstetrics department of a university hospital. Population and design This prospective study includes women with fetal growth restriction and abnormal umbilical artery Doppler results, seen between November 2009 and January 2011. Methods 31 women were divided into two groups according to the aortic isthmus blood flow pattern just before birth: anterograde (n=12) or retrograde (n=19). Main outcome measure Longitudinal measurements of fetal aortic isthmus in relation to perinatal outcome. Results Total morbidity and mortality rates were significantly higher in the retrograde flow group. There was no statistically significant difference for respiratory distress syndrome, intraventricular hemorrhage, bronchopulmonary dysplasia or necrotizing enterocolitis, but the neonatal sepsis rate was significantly higher in the retrograde flow group. An abnormal aortic isthmus flow pattern was detected approximately 1520days after umbilical artery and middle cerebral artery Doppler flow abnormalities and 37days before deterioration in ductus venosus blood flow. Conclusion We suggest that aortic isthmus Doppler measurements are useful for identifying fetal growth restriction before deterioration in ductus venosus blood flow and fetal acidosis.