Elevated levels of maternal serum alpha-fetoprotein (MSAFP) will identify a population at increased risk for specific congenital malformations, which are accurately diagnosed by amniotic fluid AFP and acetylcholinesterase. The risk for spontaneous abortion related to amniocentesis, combined with increasing confidence in the accuracy of ultrasound diagnosis, has caused us to question the need for amniocentesis in the diagnostic workup of pregnancies complicated by elevated levels of AFP in maternal serum. A retrospective study of 257 pregnancies evaluated for elevated serum AFP levels revealed 16 fetal malformations diagnosed by amniotic fluid AFP and acetylcholinesterase. Only 12 of these malformations were diagnosed on the initial ultrasound study. All malformations were diagnosed when ultrasound examination was repeated for increased acetylcholinesterase activity. Earlier gestational age at scanning, smaller defects, and pure technical failure were implicated as causes of misdiagnosis. The rate of fetal malformations identified in this high-risk population (6.23%) and the rate of ultrasound misdiagnosis (1.5% of the population with elevated levels of MSAFP) imply that amniocentesis should still be considered an essential part of the diagnostic workup in these situations.