This retrospective multicenter study represents an analysis of the intrauterine determinants of the prognosis for conotruncal anomalies. Data regarding reason for referral, presence of chromosomal or extracardiac anomalies, pregnancy and surgical outcome were recorded in 67 cases of conotruncal anomalies from three Italian referral units. Chromosomal aberrations effected 11 of the 60 (18.3%) fetuses in which a karyotype was available. Extra-cardiac malformations were present in 25/67 cases (37.3%). No chromosomal anomalies were present in fetuses with complete or corrected transposition of the great arteries. However, tetralogy of Fallot and double-outlet right ventricle were associated with chromosomal anomalies in 22% and 38% of cases, respectively, and with extracardiac anomalies in 45% and 46% of cases, respectively. Only 20 of the 67 (31%) cardiac malformations were associated with an abnormal four-chamber view. There were 28 (41.7%) terminations of pregnancy, six (8.9%) intrauterine deaths and 16 (23.8%) neonatal deaths. Seventeen neonates (25.3%) are currently alive, and 15 of these have undergone reparative surgery. The prognosis of conotruncal anomalies is poorer when the conditions is diagnosed in utero. This is mainly due to the frequent association with chromosomal and/or extracardiac anomalies, often leading to intrauterine or early neonatal death.