In this study, we sought to determine fecal cytokine levels in very preterm newborns at the onset of non-specific clinical symptoms of necrotizing enterocolitis (NEC) and decreased gastrointestinal (GI) motility. The study was approved by the Ethics Committee and the Scientific Council of the National Medical Research Center for Obstetrics, Gynecology and Perinatology named after the Academician V. I. Kulakov of Ministry of Healthcare of the Russian Federation. Each patient’s parents gave their informed consent to their child’s participation in the study. The study was conducted at the National Medical Research Center for Obstetrics, Gynecology and Perinatology named after the Academician V. I. Kulakov over the period from June 2020 to December 2022. Fecal samples from preterm neonates with gestational age ≤ 32 weeks treated at the A.G. Antonov ICU were collected daily over their first 14 days of life. Samples from 46 newborns were selected for analysis: fecal samples collected on the day of an enteral feeding intolerance episode and fecal samples from controls who had not developed non-specific clinical symptoms of NEC or decreased GI motility, collected on the day when enteral intake reached 100 ml/kg/day. Based on the results of NEC and decreased GI motility diagnosis, stool samples were retrospectively divided into 3 groups: an NEC group (n = 8), a decreased GI motility group (n = 14) and a control group (n = 24). In the fecal samples of the very preterm newborns with NEC stage ≥ II, there was a significant increase in IL-6, IL-8, IL-10, TNF-a levels at the onset of initial symptoms of the disease. At the same time, the cytokine profile of the feces of the decreased GI motility patients did not differ significantly from the control group in any of the parameters. In cases of NEC, high IL-6, IL-8, IL-10 and TNF-a levels were detected in the patients’ stool at the onset of enteral feeding intolerance, suggesting that the method under investigation (aimed at determining the pro- and anti-inflammatory profile of fecal cytokines) may be a promising new tool for differentiating NEC from decreased GI motility in very preterm newborns.