Anemia is well recognized as a marker of poor prognosis in patients with acquired heart disease and heart failure. Adults with complex congenital heart disease and ventricular dysfunction (subaortic right ventricle or single-ventricle physiology) represent a different population, because they are typically much younger and have less co-morbidity compared with patients with acquired forms of heart disease. The purpose of this study was to evaluate the prevalence and determinants of anemia in this population. Baseline hemoglobin levels were recorded at the time of the initial clinic visit, and final hemoglobin levels were those recorded before death or transplantation or at study completion. Anemia was defined as hemoglobin <135 g/L in men and <120 g/L in women. One hundred sixty-seven patients (100 men, mean age 34 +/- 8 years, mean ejection fraction 35 +/- 9%) were included, 66 with atrial switch operations, 42 with congenitally corrected transposition of the great arteries, and 59 with Fontan physiology. The mean hemoglobin level at baseline was 149 +/- 22 g/L and at follow-up was 139 +/- 29 g/L. The overall prevalence of anemia was 29% at completion. Hyponatremia, decreased renal function, and the use of warfarin were independent predictors of anemia. In conclusion, anemia is common in patients with complex congenital heart disease and ventricular dysfunction, in particular those with Fontan physiology.