A 5-year prospective prenatal study in 151 pregnancies with 152 malformed fetuses detected by ultrasound was evaluated cytogenetically. Thirty-five fetuses (23%) had abnormal karyotypes. Specific anatomical fetal malformations identified by ultrasound increase the risk for fetal chromosome abnormalities. Risks of abnormal chromosomes in the fetus are present with both single and multiple anomalies including amniotic fluid volume although the risk is increased with specific anatomical systems and multiple malformations. An abnormal fetal karyotype was present in 17% with a single anatomical abnormality and 30% when two or more anatomical systems were involved. Fetal hydrops, duodenal atresia, and omphalocele were the most specific single ultrasound anomalies; fetal hydrops, IUGR, holoprosencephaly, congenital heart disease, diaphragmatic hernia, duodenal atresia, and omphalocele were the most specific multiple anomalies with abnormal amniotic fluid volume. Termination of pregnancy occurred in 32/58 patients diagnosed prior to the 20th week of pregnancy with most (31/32) having a chromosomal anomaly or severe fetal anomaly. Fetuses terminated after the 20th week had chromosomal (7/18) or lethal fetal anomalies (11/18). The most common aneuploidies were trisomy 21, trisomy 18, and 45,X. The decision to terminate the pregnancy was based in most cases on the fetal ultrasound findings. Correlation of ultrasound and clinical findings is important for accurate genetic counselling.