Bloody stools are a particularly concerning symptom in neonates and infants. The differential diagnosis reaches from life-threatening to benign conditions. We would like to present two infants, who presented to the paediatric emergency department with bloody stools and showed pneumatosis on ultrasonography, which initially led to the suspicion of a potentially life-threatening condition. Both children had an unremarkable physical examination and both the laboratory chemical parameters, as well as the stool analyses were without abnormal findings. As in summary, there was no evidence of necrotizing enterocolitis, and Food Protein-Induced Allergic Proctocolitis (FPIAP) was considered the most likely diagnosis, an ambulant nutritional counselling was provided. As FPIAP is a clinical diagnosis, the number of cases in which pneumatosis can be detected is unclear. It is speculated that, like atopic dermatitis, food allergies alter, for example, the tight junctions and lead to an increased intestinal permeability which might result in pneumatosis intestinalis.