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.