Necrotizing enterocolitis (NEC) is the most common severe gastrointestinal emergency in neonatal period. Searching biomarkers to identify infants at greatest risk of developing NEC might be of importance for early diagnosis, effective treatment and better prognosis of NEC. Biomarkers from stool and urine attract great attention due to non-invasiveness and easy availability of fecal and urinary sampling. This article reviews the latest research progress of non-invasive biomarkers including intestinal fatty acid binding protein, serum amyloid A, complement C3a and C5a in urine; fecal lactoferrin, intestinal bacteria spectrum, fecal calprotectin, S100A12 and high mobility group box-1 protein.