Aims and Objectives: We used near-infrared spectroscopy to document changes in cerebral tissue oxygen saturation (SctO 2 ) in response to ventilation mode alterations after bidirectional Glenn (BDG; superior cavopulmonary connection) procedure. We also determined whether spontaneous ventilation have a beneficial effect on hemodynamic status, lactate and SctO 2 when compared with other ventilation modes. Materials and Methods: 20 consecutive patients undergoing BDG were included. We measured SctO 2 during three ventilator modes (intermittent positive-pressure ventilation [IPPV]; synchronized intermittent mandatory ventilation [SIMV]; and continuous positive airway pressure + pressure support ventilation [CPAP + PSV]). We, also, measured mean airway pressure (AWP), arterial blood gases, lactate and systolic arterial pressures (SAP). Results: There was no change in SctO 2 in IPPV and SIMV modes; the SctO 2 measured during CPAP + PSV and after extubation increased significantly (60.5 ± 11, 61 ± 10, 65 ± 10, 66 ± 11 respectively) ( P < 0.05). The differences in the SAP measured during IPPV and SIMV modes was insignificant; the SAP increased significantly during CPAP + PSV mode and after extubation compared with IPPV and SIMV (109 ± 11, 110 ± 12, 95 ± 17, 99 ± 13 mmHg, respectively) ( P < 0.05). Mean AWP did not change during IPPV and SIMV modes, mean AWP decreased significantly during CPAP + PSV mode (14 ± 4, 14 ± 3, 10 ± 1 mmHg, respectively) ( P < 0.01). Conclusions: The SctO 2 was higher during CPAP + PSV ventilation and after extubation compared to IPPV and SIMV modes of ventilation. The mean AWP was lower during CPAP + PSV ventilation compared to IPPV and SIMV modes of ventilation.