Necrotizing enterocolitis (NEC) is a severe disease of the gastrointestinal tract of pre-term babies and is thought to be related to the physiological immaturity of the intestine and altered levels of normal bacteria in the gut. Studies have shown a reduced incidence and severity of NEC in neonates treated with probiotics, which are non-pathogenic species of bacteria that benefit the host. The protective potential of probiotics is analyzed using a mathematical model. Ordinary differential equations are used to track the populations of pathogenic and probiotic bacteria in the intestinal lumen and in the blood/tissue. The permeability of the intestinal epithelial layer is treated as a variable, and the role of the inflammatory response is included. The model predicts that in the presence of probiotics, health is restored in many cases that would have been otherwise characterized as disease states. However, in some instances, the model predicts that probiotics can lead to an efflux of bacteria from the intestine into the blood, triggering an overwhelming inflammatory response. The model is used to evaluate this paradox associated with probiotic treatment, which has also been seen clinically, by pinpointing conditions under which this therapy may be beneficial or detrimental.