Circulatory and metabolic homeostasis in patients with hypoplastic left heart syndrome is dependent on a delicate balance between systemic and pulmonary blood flow. Hypocarbia can result in a marked decrease in pulmonary vascular resistance accompanied by pulmonary overcirculation, systemic hypotension, metabolic acidosis, and death. This report illustrates that early and precise control of the arterial carbon dioxide tension using inspired carbon dioxide can be effective in preventing or treating instability arising during management of a patient with hypoplastic left heart syndrome.