Bloody stools in the newborn may be a clue for several clinical entities of varying severity ranging from a transient hematochezia to food protein induced allergic proctocolitis (FPIAP) or necrotizing enterocolitis (NEC). To distinguish among them at an early stage is challenging, but crucial, as the treatment and prognosis are different. We conducted a monocentric retrospective study including all preterm infants admitted to the NICU of the Vittore Buzzi Children’s Hospital (Milan) with bloody stools from December 2022 to May. Patients diagnosed with NEC exhibited a significantly lower eosinophil count and higher procalcitonin levels than both patients with CMPA and patients with transient hematochezia, as well as a statistically significant increase in pathological features at abdomen ultrasounds and abdominal X-rays. In contrast, no Lab markers or imaging have been demonstrated to be useful in distinguishing between transient hematochezia and FPIAIP. Thus, after excluding a diagnosis of NEC the only way to confirm the FPIAP is the oral food challenge, which can be performed even in premature newborns presenting blood stools, otherwise healthy, under medical supervision, in order to identify infants who may benefit from a cow’s milk free diet.