Intensive cardiac management such as pharmacological intervention for ductal patency (indomethacin and/or mefenamic acid for closure and prostaglandin E1 for maintenance) and palliative or corrective surgery is a standard treatment for congenital heart defects. However, whether it would be a treatment option for children with trisomy 13 or trisomy 18 syndrome is controversial because the efficacy on survival in patients with these trisomies has not been evaluated. We retrospectively reviewed 31 consecutive neonates with trisomy 13 or trisomy 18 admitted to our neonatal ward within 6 hr of birth between 2000 and 2005. The institutional management policies differed during three distinct periods. In the first period, both pharmacological ductal intervention and cardiac surgery were withheld. In the second, pharmacological ductal intervention was offered as an option, but cardiac surgery was withheld. Both strategies were available during the third period. The median survival times of 13, 9, and 9 neonates from the first, second, and third periods were 7, 24, and 243 days, respectively. Univariate and multivariate analyses confirmed that the patients in the third period survived significantly longer than the others. Intensive cardiac management consisting of pharmacological intervention for ductal patency and cardiac surgery was demonstrated to improve survival in patients with trisomy 13 or trisomy 18 in this series. Therefore, we suggest that this approach is a treatment option for cardiac lesions associated with these trisomies. These data are helpful for clinicians and families to consider in the optimal treatment of patients with these trisomies.