In premature neonates, bloody stools and/or abdominal distension with feeding intolerance may be inaugural signs of necrotizing enterocolitis (NEC). We assessed the ability of near-infrared spectroscopy (NIRS) to distinguish those neonates with NEC soon after the occurrence of these symptoms. We prospectively collected NIRS measurements of abdominal and cerebral regional tissue oxygen saturation (r-SO2), with values masked by an opaque cover. Two physicians, blinded to the NIRS data, determined whether the gastrointestinal symptoms were related to NEC 10 days after symptom onset. Forty-five neonates with mean (standard deviation [SD]) gestational, birth weight and postnatal ages of 31 (3.9) weeks, 1,486 (794) g, and 18 (14) days were enrolled over 30 months. Gastrointestinal symptoms were related to NEC in 23 patients and associated with other causes in 22. Analysis of the 48 hours of monitoring revealed comparable abdominal r-SO2 and splanchnic-cerebral oxygenation ratio (SCOR) in patients with and without NEC (r-SO2: 47.3 [20.4] vs. 50.4 [17.8], p = 0.59, SCOR: 0.64 [0.26] vs. 0.69 [0.24], p = 0.51). Results were unchanged after NIRS analysis in 6-hour periods, and restriction of the analysis to severe NEC (i.e., grade 2 and 3, 57% of the NEC cases). In this study, NIRS monitoring was unable to individualize NEC in premature infants with acute gastrointestinal symptoms.