Historically, outcomes of patients with heterotaxy syndrome and congenital heart disease have been poor. Published series include patients treated over many decades or focus on specific patient/operative subgroups. This study was performed to evaluate midterm outcomes and determine anatomic risk factors for death in patients with all types of heterotaxy syndrome treated after 1985. We reviewed all infants with heterotaxy born between 1985 and 1997, presenting to one institution at <6 months age, followed for > or =5 years. Of 102 study patients (46 with asplenia phenotype, 56 with polysplenia phenotype), 48 (47%) died at a median age of 0.6 months, 12 without intervention. Survivors were followed for a median of 12.8 years (5-21.7 years). Independent predictors of mortality included obstructed totally anomalous pulmonary venous connection (TAPVC) (OR, 7.8; 95% CI, 1.9-32.9; p = 0.005), mild or greater atrioventricular (AV) valve regurgitation at presentation (OR, 3.5; 95% CI, 1.0-12.1; p = 0.03), and common AV canal (OR, 3.1; 95% CI, 1.1-8.5; p = 0.03). Sixteen patients developed pulmonary vein stenosis at a median age of 2 months, with 5 (31%) alive at follow-up. In patients with TAPVC, the mean indexed sum of pulmonary vein diameters was lower among patients who died than in survivors (42.3 +/- 8.3 vs 49.5 +/- 10.1 mm/m2; p = 0.02). Mortality remains high among patients with heterotaxy treated in the modern surgical era, particularly those with obstructed TAPVC. Pulmonary vein stenosis is common after repair of TAPVC in patients with heterotaxy, may be diagnosed beyond infancy, and is associated with poor outcomes.