Trisomy 13 and 18 are associated with congenital heart disease. Cardiac palliation has been reported in the literature, but is not usually done in this population. Thus, a multi-disciplinary team may experience controversy in formulating a care plan that includes cardiac intervention. Our objective was to determine differences in recommendations for cardiac intervention in this population between physicians specializing in pediatric cardiac critical care, neonatology, and genetics. A web-based survey was performed between April 2007 and August 2008. This survey evaluated surgical and transcatheter cardiac palliations that had been performed for individuals with trisomy 13 or 18 at the respondent's institution, the respondent's recommendations for cardiac intervention in hypothetical symptomatic patients with trisomy 13 or trisomy 18 and the influence of parental preference on these recommendations. Eight hundred fifty-nine responses were obtained from a primarily academic practice setting (59%). Cardiologists were most likely to recommend intervention; low risk interventions were recommended by 32% of cardiologists, 7% of neonatologists and 20% of geneticists. Parental request to intervene resulted in a 3 fold increased in the likelihood of all specialist recommending intervention. Counseling of families frequently occurred by multiple sub specialists (50%) and there was frequently (71%) a difference in opinion. Individuals with trisomy 13 or 18 are receiving cardiac intervention at many institutions. Cardiologists were more likely than geneticists or neonatologists to recommend intervention on all heart lesions other than single ventricle palliation which no specialists recommended. Parental wishes that "everything be done" significantly influenced all specialists' recommendations.