Background: Several efforts are under way to conduct quality-improvement initiatives in pediatric cardiology and cardiac surgery. Our goal was to develop an objective prioritization scheme for such initiatives based on encounter frequency and relative contribution of quality measures of morbidity (and associated variances), particularly in the setting of low mortality. Methods: We identified patients in the Pediatric Health Information System in Risk Adjustment for Congenital Heart Surgery 1 category 1 to 6 for 32 pediatric cardiac surgical procedures conducted between 2003 and 2011 (n = 67,550). These were examined for their overall contribution to mortality, intensive care unit and hospital lengths of stay (coefficient of variation and excess days), adverse events, and readmission rates. A ranking scheme was created on the basis of the outcome measures. Then we ordered the procedures across metrics to develop a prioritization scheme. Results: Observed mortality rates were consistent with published rates. A few procedures accounted for significant variation in hospital and intensive care length of stay across the hospitals. Likewise, a few procedures accounted for most excess days of stay and readmission rates. Up to 60% of the hospital stay was accounted for by intensive care unit stay. Although there was a linear relationship between adverse event rates and Risk Adjustment for Congenital Heart Surgery 1 categories, a few procedures once again accounted for disproportionate event rates within and across their respective Risk Adjustment for Congenital Heart Surgery 1 categories. Conclusions: A small number of procedures account for a substantial burden of morbidity, even among low mortality risk groups. Consideration should be given to using such objective prioritization schemes to develop targeted quality-improvement measures.