Many infants with congenital heart disease undergo palliative shunt procedures. In our center, cryopreserved saphenous vein and polytetrafluoroethylene (PTFE) are used as grafts to construct these shunts. In this retrospective review, we compare morbidity, mortality, and freedom from reoperation associated with the use of these graft materials. We conducted a retrospective study of 136 consecutive patients who were palliated with shunts between 2006 and 2015. A total of 136 patients were identified, 9 had incomplete data; thus, 127 patients were included: 69 saphenous and 58 PTFE. The cohorts were matched with respect to birth weight, gestational age, age and weight at time of surgery, and underlying cardiac condition. There were 15 (12%) deaths in the study cohort with no intraoperative mortality. Thrombosis was seen in 5.2% (2/38) of the saphenous modified Blalock-Taussig shunt (mBTS) group and 20.6% (14/68) of those with PTFE mBTS. There was no thrombosis in the central shunt group. Freedom from reoperation was 83% in the saphenous vein group and 81% in the PTFE group. There was no difference in overall morbidity or mortality, although thrombosis was significantly less in the saphenous vein group. Cryopreserved saphenous vein is a safe alternative, either as a mBTS or as a central shunt.