Introduction: Congenital heart disease (CHD) is one of the most common birth defects. Cerebral (cStO₂) and renal (rStO₂) saturations measured by near-infrared spectroscopy (NIRS) and the corresponding fractional tissue oxygen extraction (FTOE) during the first week of life in neonates with CHD are described comparing those with and without diastolic steal. METHODS: Single-center prospective cohort study (Montreal Children's Hospital, Montreal, QC, Canada) was conducted, including neonates >34 weeks with CHD without chromosomal anomalies. CStO₂/rStO₂ was monitored from enrollment until day 7 of life. FTOE was calculated using systemic saturation (SpO₂) as [SpO₂ - (cStO₂ or rStO₂)]/SpO₂. Daily echocardiography was performed during the monitoring period. Random mixed-effects models were constructed to assess the association between NIRS/FTOE and the presence of retrograde postductal aortic flow on last available echocardiography. RESULTS: Among 49 included neonates, 27 (55%) exhibited retrograde flow in the postductal aorta on the last day of monitoring. Prostaglandin exposure was 100% in the retrograde group vs. 27% in the non-retrograde group. CStO₂/rStO₂ progressively declined in neonates with CHD over the first week of life. Retrograde aortic flow was associated with negative cStO₂ (β = -9.1%, 95% CI [-14.3; -3.8]) and rStO₂ (β = -8.4%, 95% CI [-14.5; -2.3]). Cerebral FTOE was lower in the non-retrograde group, while renal FTOE was similar between groups. CONCLUSION: During the first week of life, neonates with CHD who displayed retrograde aortic flow exhibited lower cStO₂ and rStO₂ as well as higher cerebral FTOE. Future studies should evaluate whether these markers in neonates with CHD are modifiable factors that could influence cerebral or renal injury when addressed.