Background Cardiopulmonary bypass induces marked and persistent depression of circulating thyroid hormones in infants and children, possibly contributing to postoperative morbidity. Clinical studies have evaluated parenteral triiodothyronine supplementation after cardiopulmonary bypass in children. However, these investigations had relatively small subject numbers as well as age and diagnosis heterogeneity, thereby limiting ability to determine clinical effect. A double-blind, randomized, placebo-controlled trial is needed to define clinical safety and efficacy of triiodothyronine supplementation in infants. Methods and results The Triiodothyronine for Infants and Children Undergoing Cardiopulmonary Bypass (TRICC) study is a multicenter, randomized, clinical trial designed to determine safety and efficacy of triiodothyronine supplementation in children <2 years of age undergoing surgical procedures for congenital heart disease. Duration of mechanical ventilation after completion of cardiopulmonary bypass is the primary clinical outcome parameter with multiple secondary clinical and hemodynamic parameters. Nearly 200 patients will be randomly assigned to receive either triiodothyronine or placebo. Patient assignment will be performed using a stratified block randomization according to specific preoperative diagnosis. Conclusions The TRICC study will provide important data regarding the efficacy and safety of triiodothyronine in this age-specific population undergoing surgery for congenital heart disease.