We recently validated a method of quantifying systemic to pulmonary arterial collateral flow using phase-contrast magnetic resonance imaging velocity mapping (PC-MRI). Cross-sectional data suggest decreased collateral flow in patients with total cavopulmonary connections (TCPC) compared to those with superior cavopulmonary connections (SCPC). However, no studies have examined serial changes in collateral flow from SCPC to TCPC in the same patients. We sought to examine differences in collateral flow between patients with superior cavopulmonary connections (SCPC) and total cavopulmonary connections (TCPC). We quantified collateral flow by two independent measures from 250 single ventricle studies in 219 different patients, (115 SCPC and 135 TCPC studies, 31 patients with both) and 18 controls, during routine studies using through-plane PC-MRI. Collateral flow was indexed to body surface area, aortic flow and pulmonary venous flow. Regardless of indexing method, SCPC patients had significantly higher collateral flow than TCPC patients (1.64±0.8 vs. 1.03±0.8 L/min/m2, p<0.001). In 31 patients who had serial exams, collateral flow as a fraction of aortic flow increased early after TCPC completion. In TCPC patients, indexed collateral flow demonstrated a significant negative correlation with time from TCPC. In conclusion, both SCPC and TCPC patients demonstrate substantial collateral flow, with SCPC patients having higher collateral flow than TCPC patients overall. Based on the paired subset analysis, collateral flow does not decrease in the short term after TCPC completion and trends toward increasing. In the long term, however, collateral flow decreases over time after TCPC completion.