In this study, we tested our hypothesis that thyroid function is impaired and contributes to perturbed hemodynamics in patients after Fontan operation. Cardiac catheterization and blood tests for thyroid function were performed in 37 patients who underwent a Fontan operation. Among them, 12 patients (33%) had subclinical thyroid dysfunction with an elevated thyroid-stimulating hormone level despite normal thyroxine levels. Thyroid-stimulating hormone levels were significantly correlated with central venous pressure (p <0.01, R² = 0.3), and patients with subclinical hypothyroidism showed significantly elevated γ-glutamyltransferase level, an indicator of liver congestion, compared with the other patients (125.6 ± 12.2 vs 67.6 ± 4.6 IU/L, p <0.01). In addition, the levels of free triiodothyronine, an effective thyroid hormone, were significantly lower in patients with subclinical hypothyroidism than in those with normal thyroid function (3.1 ± 0.1 vs 3.5 ± 0.1 pg/dl, p <0.01). The free triiodothyronine level was significantly and negatively correlated with the relaxation time constant (p = 0.03) and brain natriuretic hormone (p <0.01) level and positively correlated with the cardiac index (p = 0.04). In conclusion, venous congestion in Fontan patients may cause thyroid dysfunction, which can be responsible for decreased ventricular function and cardiac output in Fontan patients. Thus, thyroid function should be routinely monitored after Fontan surgery.