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Mechanical mitral valve replacement in infants and young children is associated with substantial morbidity and mortality. Lifelong anticoagulation is required, with all the accompanying challenges of maintaining levels in infants and children whose dietary input continually changes. Even with careful control of all aspects that can perturb the coagulation cascade, these patients have a substantial lifelong risk of thrombotic and hemorrhagic complications that can also affect the durability of the valve. Anticoagulation is usually achieved utilizing warfarin with the degree of anticoagulation measured via the international normalized ratio (INR). Unfortunately, in some cases, the INR can be falsely elevated and lead to inappropriate reassurance. We describe a 4-year-old patient with complex congenital heart disease palliated via a single ventricular pathway with a mechanical atrioventricular valve replacement. The patient experienced acute valvular thrombosis while receiving warfarin with INR at target levels. Chromogenic factor X (CFX) levels were discordant with INR measurements, suggesting a subtherapeutic level of anticoagulation despite maintaining the standard INR target. Therefore, CFX levels were used to interpret INR measurements and guide an individualized approach to anticoagulation. We propose a new role of CFX: to verify and guide warfarin anticoagulation in high-risk pediatric patients including those undergoing mechanical mitral valve replacement.