Objective: Neurologic impairment is frequently observed in children with congenital heart disease. Impairment in cerebrovascular carbon dioxide reactivity (CO2R) is related with poor neurologic outcomes. The present study examined CO2R measured with transcranial Doppler (TCD) and near-infrared spectroscopy (NIRS) in children with ventricular septal defect undergoing cardiac surgery. Design: Prospective, paired controlled study. Setting: Operating room of a tertiary care center. Participants: Twenty children with ventricular septal defect and younger than 1 year were enrolled, and 17 children were studied (age: 6.0 ± 2.0 mo, weight 5.9 ± 1.0 kg). Intervention: After induction of anesthesia and tracheal intubation, the lungs were ventilated and mechanical ventilation was initiated. Partial pressure of end-tidal carbon dioxide (PETCO2) was adjusted at 4 different levels (30, 35, 40, and 45 mmHg). Measurements and Main Results: Paired measurements of middle cerebral artery mean blood flow velocity (VMCA) by TCD and tissue oxygen index (TOI) by NIRS were recorded at each level of PETCO2. CO2R was calculated as the percentage change of VMCA and TOI per mmHg change in PETCO2. Systemic hemodynamic parameters were recorded. As PETCO2 rose from 30 to 45 mmHg, VMCA and TOI increased linearly (p < 0.001 for both), and CO2R-TCD and CO2R-NIRS were calculated to be 2.8% ± 0.9%/mmHg and 1.2% ± 0.3 %/mmHg, respectively. CO2R-NIRS was significantly lower compared with CO2R-TCD (p < 0.001). Significant correlations were found between VMCA and TOI (r = 0.487; p < 0.001) and between ΔVMCA and ΔTOI (r = 0.693; p < 0.001), but not between CO2R-TCD and CO2R-NIRS (r = 0.18; p = 0.24). With the increase of PETCO2, cardiac index, systemic vascular resistance index, and mean arterial pressure remained constant (p > 0.05 for all) and the heart rate decreased significantly (p = 0.018). Conclusions: During anesthesia, CO2R remains preserved in children with a ventricular septal defect. Even though there is lack of correlation between CO2R-TCD and CO2R-NIRS, changes in TOI and VMCA were correlated as the PETCO2 changed. NIRS may be used as a surrogate to investigate CO2R when the ultrasound window is poor. © 2019 Elsevier Inc.