Patients with single ventricle heart disease undergoing staged palliation are exposed to ionizing radiation from multiple medical sources. We sought to quantify typical radiation burden in this population and identify risk factors for increased exposure. A retrospective review was performed of single ventricle patients surgically palliated at our institution, in which all studies utilizing ionizing radiation occurring from birth through Fontan completion were compiled. Thirty-eight patients were followed for a median of 33 months. A median of 59 radiation events occurred during follow-up, with a median cumulative effective dose of 25.7 milliSieverts (mSv). On average, cardiac catheterization accounted for 4% of radiation encounters but comprised 78% of total radiation exposure. In a multivariate model, factors associated with increased total radiation exposure included pulmonary artery (PA) stenosis requiring intervention (p = 0.005) and systemic right ventricle (p = 0.02). Risk factors for increased exposure from catheterization included heterotaxy syndrome (p = 0.007), re-coarctation (p = 0.003), and PA stenosis (p = 0.02). At our institution, many single ventricle patients are exposed to substantial radiation throughout staged palliation, most of which derives from cardiac catheterization. PA stenosis was identified as a risk factor for increased total and catheterization-based exposure. As patient survival improves, awareness of this scale of radiation exposure at a vulnerable period is imperative.