The maintenance of an adequate oxygen supply to tissues after congenital heart surgery is essential for good outcomes. The objective of this study was to assess the usefulness of near-infrared spectroscopy (NIRS) for estimating central venous oxygen saturation (ScvO₂) using both cerebral and renal measurements, explore its relation with cardiac output measurements and check its ability to detect low cardiac output. A prospective observational pilot study was conducted in patients weighing <10 kg undergoing cardiopulmonary bypass surgery. Spectroscopy probes were placed on the forehead and renal area, and serial cardiac output measurements were obtained by femoral transpulmonary thermodilution over the first 24 h after surgery. In the 15 patients studied, ScvO₂ was correlated with cerebral (r = 0.58), renal (r = 0.60) and combined (r = 0.71) measurements. Likewise, the systolic index was correlated with the NIRS signals: cerebral (r = 0.60), renal (r = 0.50) and combined (r = 0.66). Statistically significant differences were found in the NIRS measures registered in the 29 low cardiac output events detected by thermodilution: cerebral: 62 % (59–65) versus 69 % (63–76); renal: 83 % (70–89) versus 89 % (83–95); and combined 64 % (60–69) versus 72 % (67–76). In our series, combined cerebral and renal monitoring was correlated with central venous oxygen saturation and cardiac output; low cardiac output detection associated a different spectroscopy pattern.