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Background: Inflammatory mediators including IL-6 and TNF-alpha, may play a significant role in NEC. It is difficult to differentiate feeding intolerance (FI) or suspected NEC (Stage 1) clinically on initial presentation from NEC (Stage II and III). Some of these infants may receive unnecessary medical interventions. Objective: To examine whether measurements of circulating IL-6 and TNF-alpha could differentiate between infants with FI and infants with NEC. Methods: 70 infants were enrolled in the study. Blood samples were obtained during weeks 2 to 3 in control infants, or at the onset of FI or NEC. Cytokines were assayed on a DPC Immulite system. Statistical evaluation of the different groups was carried out using ANOVA, Student-t and Wilcoxon tests. Results: Blood samples were collected from 40 normal control infants, 18 infants with FI and 12 infants with NEC. The mean age of sampling from controls was 18.5 days, from FI infants was 16.5 days and from NEC infants 16.9 days. There was no correlation between control values of IL-6 or TNF-alpha and gestational age (GA). There was no statistically significant difference in the TNF-alpha between the three groups, however IL-6 was significantly increased in infants with NEC. Conclusion: Measurement of IL-6 may be useful in distinguishing infants with FI from NEC. Our observations also suggest that the pathophysiology of FI is different from that of NEC. Table