The fecal occult blood test (FOBT) is a screening tool for hematochezia. This study aims to summarize the clinical features associated with a positive FOBT in neonates and to explore some clues for the underlying causes. Combination with other clinical information, identifying the possible etiology is more likely and could be useful for choosing an effective therapeutic strategy. The medical records of 282 neonates with positive FOBTs from January 1 to July 31, 2016, were collected and retrospectively analyzed. The total incidence rate of FOBT positivity in neonates was 6.2%. Among these patients, 71 (25.2%) neonates had false-positive FOBTs, whereas 211 (74.8%) neonates had intraintestinal sources of hematochezia. Necrotizing enterocolitis (NEC, 20.9%), structural abnormalities of gastrointestinal tract (SAGT, 12.4%), and suspected food allergy (sFA, 10.6%) were the most common causes of neonatal hematochezia. It indicated that FOBT-positive neonates with NEC were more likely to suffer due to a younger gestational age, lower birth weight, and lower weight on admission than the neonates with other conditions. The proportions of neonates with bloody stool (90.0%) and diarrhea (63.3%) in the sFA group were markedly higher than those in the other groups. However, in the SAGT group, emesis (94.3%) and abdominal distension (80.0%) were evidently higher, usually accompanied by a relatively poor response (60.0%) and weakened bowel sounds (48.6%). Furthermore, the higher incidences of poor response (72.1%), abdominal distension (71.2%), bloody stools (64.4%), and weakened bowel sounds (62.7%) were observed in the NEC group. Due to the complicated etiology associated with a positive FOBT, the analyzed indexes were combined with other clinical features to identify the likely causes of neonatal hematochezia. Because NEC, sFA and SAGT show similar clinical manifestations and can occasionally transform into each other, close and frequent observation is crucial for timely intervention to achieve a better prognosis. Although it failed to provide an early warning of severe disease through FOBT, and the early intervention for FOBT might not decrease NEC, sFA, structural bowel injuries, or any other complications, newborn FOBT positive reminds medical staff to be alert to the related diseases including NEC, SAGT and sFA, by closer observation and follow-up.