OBJECTIVE To test the hypothesis that patients with complex congenital heart disease who have undergone Fontan palliation have low total cholesterol, low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) levels. METHODS We retrospectively reviewed the random serum lipid profiles obtained at cardiology clinic visits between May 2010 and November 2011 in patients who had undergone the Fontan procedure. We compared these serum lipid levels against age- and sex-matched established normal data from the Third National Health and Nutrition Examination Survey. RESULTS Eighty-eight patients who had undergone the Fontan procedure also had laboratory test data obtained during their visits. Median total cholesterol level in the Fontan group was 127 mg/dL (IQR, 116-144 mg/dL), median HDL-C was 40 mg/dL (IQR, 33-45 mg/dL), median non-HDL-C was 86 mg/dL (IQR, 76-109 mg/dL), and median LDL-C was 66 mg/dL (IQR, 57-83 mg/dL). Total cholesterol, LDL-C, non-HDL-C, and HDL-C levels were significantly lower in patients who had undergone a Fontan procedure compared with age- and sex-matched normal individuals (mean z-score, -1.4, -1.2, -1.0, and -1.0 respectively; all P<.0001). Cholesterol levels were below the 25th percentile for age and sex for total cholesterol in 82% of patients, for LDL-C in 76%, for non-HDL-C in 67%, and for HDL-C in 57%. CONCLUSIONS Patients who have undergone the Fontan procedure have significantly lower serum total cholesterol, LDL-C, HDL-C and non-HDL-C levels than age- and sex-matched normal individuals. Although the implications of this finding are unknown, it raises the possibility of abnormalities in cholesterol absorption, synthesis, or catabolism in this patient population.