Objective: Thyroid hormone has important effects on cardiovascular performance. This study was performed to evaluate the changes in levels of triiodothyronine following the first stage of reconstruction for hypoplastic left heart syndrome. Methods: We enrolled 14 newborns with hypoplastic left heart syndrome scheduled for first stage reconstruction. Blood samples were obtained pre-, intra-, and post-operatively. Levels of free and total triiodothyronine were determined by radioimmunoassay. Statistical comparison was performed using Wilcoxon's signed rank test. Results: The levels of free triiodothyronine decreased from a baseline of 355 ± 31 pg/dl to 205 ± 21 pg/dl upon the institution of bypass, and declined to a level of 135 ± 9 pg/dl at 24 hours postoperatively. Similarly, levels of total triiodothyronine decreased from 101 ± 15 ng/dl to 65 ± 4 ng/dl upon the institution of bypass, and continued to decline during the first 24 hours postoperatively. Levels of free and total triiodothyronine had returned to baseline by the fifth postoperative day. Conclusions: The data demonstrate significant decreases in levels of free and total triiodothyronine during the early postoperative period. These changes in levels of thyroid hormone may have adverse effects on cardiac function during this phase of recovery.