OBJECTIVE To compare the clinical characteristics of necrotizing enterocolitis (NEC) and food protein-induced enterocolitis (FPIES) when both have pneumatosis intestinalis (PI) and to identify them. METHODS Analytical study. METHODS Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China, from January to December 2019. METHODS Medical data of neonates, who were diagnosed with NEC (Bell's Stage ≥2a) or FPIES, were retrospectively evaluated. All included infants had abdominal radiographic PI positive. According to the infants' diagnoses, they were classified into groups NEC and FPIES. The clinical characteristics of NEC and FPIES were compared to find the differences. RESULTS A total of 293 infants were included, of which 205 were diagnosed with NEC and other 88 were FPIES. NEC was characterised by low birth weight (BW), gestational age (GA) and onset time; NEC had higher rates of mother's antenatal steroid therapy, formula feeding, sepsis, and anemia. NEC and FPIES both had a set of similar signs and symptoms which varied depending on the severity of the disease, except for abdominal tenderness and absent bowel sounds only observed in NEC. The rates of continuous elevated C-reactive protein (CRP) and thrombocytopenia were also higher in NEC than in FPIES (p<0.05). CONCLUSIONS When PI-positive, although infants diagnosed with NEC or FPIES lack specific signs and symptoms, there are still clinical characteristics that need to be focused on: risk factors (BW, GA, onset time, mother's antenatal steroid therapy, formula feeding, sepsis, and anemia), abdominal signs (abdominal tenderness and absent bowel sounds), the results of CRP and platelet, which may help clinicians to identify them. BACKGROUND Necrotizing enterocolitis, Food protein-induced enterocolitis syndrome, Pneumatosis intestinalis, Neonate.