Cardiac intervention remains controversial in patients with trisomy 13 and 18 and little is known about factors that may affect outcomes. The goal of this study was to evaluate preoperative factors and surgical approach with respect to outcomes in these patients. Patients with congenital heart disease and trisomy 13 or 18 presenting to our institution from 2004 through 2015 were retrospectively reviewed. Patients were grouped into complete intervention, palliated intervention, and non-intervention. Pre-intervention variables, timing and type of intervention, post-intervention outcomes, and survival were recorded and comparisons were made between the groups. Of 34 patients, 18 cardiac interventions were performed. Complete repair was performed in 11(61%) and palliation in 7(39%). Median age for complete repair was 9.2 vs. 1.7 months in palliated patients (p < 0.001) and palliated patients were smaller (median 2.5 vs. 5.2 kg, p < 0.001). All patients who underwent complete repair survived to discharge compared to only 57% of patients that were palliated (p = 0.04). Palliated patients had longer intubation and time to discharge (p < 0.05). Survival at last follow-up was greater in the complete repair group compared with palliated patients and non-intervention patients (72, 14, and 18%, p = 0.009) with a longer median length of survival in the complete repair group (p = 0.002). In our group of trisomy 13 and 18 patients, those able to undergo complete repair had improved outcomes. Patients undergoing complete repair were older and bigger; this suggests that delaying intervention and optimizing the likelihood of complete repair may be beneficial.