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Hypoplastic left heart syndrome (HLHS) is a highly resource-intensive diagnosis. Geographic variation in cost and length of stay (LOS) in HLHS is not well described. Neonates diagnosed with HLHS between 2000 and 2012 were identified using the Kids’ Inpatient Database. Hospitalizations were stratified into two groups: (1) birth and (2) secondary. United States regional differences in hospital charges and LOS were compared using adjusted linear regression. Of 2431 birth hospitalizations, 449 neonates (18.5%) died while inpatient and mortality rates differed by region (p = 0.02). After birth, 40.5% (n = 985) of neonates were transferred; transfers were most common in the Midwest (p < 0.0001). Adjusted average LOS was shortest in the West and longest in the South (26.1 days; 95% CI 24.0, 35.1 vs. 34.9 days; 95% CI 31.8, 38.1). Average adjusted charges were lowest in the Northeast ($324,600; 95% CI $271,400, $377,900) and highest in the West ($400,500; 95% CI $346,700, $454,300, p = 0.05). Among 1895 secondary hospitalizations, 24.9% of neonates died as inpatients, and the average adjusted LOS was shortest in the West (26.8 days; 95% CI 23.9, 29.7) and longest in the South (38.5 days; 95% CI 34.4, 42.4). Average adjusted charges were lowest in the Northeast ($326,900; 95% CI $270,700, $383,100) and highest in the South ($505,900; 95% CI $450,200, $561,500, p < 0.0001). Significant geographic variations in mortality, LOS, and hospital charges exist in care of US HLHS neonates. Reducing variation in care should remain a priority in national quality efforts in congenital heart disease. [ABSTRACT FROM AUTHOR]