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Background Congenital heart disease consumes significant health care resources; however, there are limited data regarding factors impacting resource utilization. The purpose of this study was to evaluate variation between centers in total hospital costs for four congenital heart operations of varying complexity, and associated factors. Methods and Results The Premier Database was used to evaluate total cost in children undergoing isolated atrial septal defect (ASD) repair, ventricular septal defect (VSD) repair, tetralogy of Fallot (TOF) repair, or arterial switch operation (ASO) from 2001-2007. Mixed models were used to evaluate the impact of center on total hospital costs adjusting for patient and center characteristics and length of stay (LOS). A total of 2,124 patients were included: 719 ASD (19 centers), 792 VSD (20 centers), 420 TOF (17 centers), and 193 ASO (13 centers). Total cost increased with complexity of operation from median $12,761 (ASD repair) to $55,430 (ASO). In multivariable analysis, models which accounted for center effects vs. those which did not performed significantly better for all four surgeries (all p ≤ 0.01). The proportion of total cost variation explained by center was 19% (ASD repair), 11% (VSD repair), 6% (TOF repair), and 3% (ASO). Higher volume centers had significantly lower hospital costs for ASD and VSD repair, but not for TOF repair and ASO. Conclusions Total hospital costs varied significantly by center for all congenital heart surgeries evaluated, even after adjustment for patient and center characteristics and LOS. Differences among centers were most prominent for lower complexity procedures.