Diminished cardiac function is a common manifestation following the modified Fontan procedure. Since thyroid hormone has important effects on cardiovascular function, the present study was undertaken to evaluate changes in thyroid hormone levels following this operation. A control group consisting of children undergoing open heart procedures other than a Fontan procedure was also evaluated. Serum total and free triiodothyronine (T3), total and free thyroxine (T4), thyroid stimulating hormone (TSH), and thyroglobulin were measured by immunoassays. The Fontan group demonstrated an initial increase in free T4, while free T3, total T3, total T4, TSH, and thyroglobulin were reduced. Over the subsequent days, free T4 decreased to below the preoperative value. By the fifth and eighth postoperative days, free T3, total T3, free T4, and total T4 remained reduced, while TSH and thyroglobulin began increasing toward the preoperative levels. The control group also demonstrated decreases in free T3 and TSH. However, these values had returned to baseline by the fifth postoperative day. The results indicate that children undergoing open heart surgery have suppression of the pituitary-thyroid axis, and that this is prolonged in patients undergoing Fontan procedure. The decreased levels of T3 following Fontan procedure may have adverse effects on the recovery of patients undergoing this operation.