OBJECTIVES: To document cerebral saturation in response to alterations in mechanical ventilation in infants with bidirectional superior cavopulmonary connection. DESIGN: Prospective study. SETTING: Pediatric cardiovascular intensive care unit. PATIENTS: Children with functional single ventricle who have undergone bidirectional superior cavopulmonary connection. INTERVENTIONS: We measured cerebral oxygenation using near-infrared spectroscopy in response to three ventilator interventions (change 50% from baseline): a) hyperventilation with increased tidal volume; b) hyperventilation with increased respiratory rate; and c) hypoventilation by decreased respiratory rate. Physiologic variables documented were cerebral oxygenation index (rSO2i), arterial pH, and PCO2. MEASUREMENTS AND MAIN RESULTS: Ten patients (eight males and two females) underwent placement of bidirectional superior cavopulmonary connection. There were no mortalities. The mean age was months 8.6 (+/-2.1) months. Hyperventilation (tidal volume increase) caused an increase in pH from 7.35 to 7.42 (p = .001), a decreased PCO2 from a baseline 45.9 to 33.9 mm Hg. (p = .002), a decrease in rSO2i from 64.4 to 52.0 (p < .001), and a decreased Po2 from 52.8 to 46.9 mm Hg (p = .008). Hyperventilation (respiratory rate increase) caused increased pH from 7.35 to 7.39 (p = .002), decreased PCO2 from a baseline 41 to 37 mm Hg. (p = .021), decreased rSO2i from 65.9 to 56.7 (p = .007), and decreased PO2 from 54.9 to 48.9 mm Hg (p = .006). Hypoventilation (respiratory rate decrease) did not change pH did not change from baseline 7.35. The PCO2 increased from 40.8 to 42, and the rSO2i increased from 64.0 to 68.6 (p = .004). CONCLUSIONS: Hyperventilation can potentially cause a decrease in cerebral oxygenation and should be avoided in children with bidirectional superior cavopulmonary connection. Normoventilation and mild respiratory acidosis, however, preserve cerebral oxygenation in these patients.