It is our postulate that the field of prebiotic research has until now been characterized by a one-view-fits-all approach, implicating that if a putatively prebiotic compound is good for something, it is good for everything. One area where this implication has been proved insufficient regards the putative preventive effect of prebiotics against intestinal pathogenic bacteria. Although indeed most evidence on effects of prebiotics against infections is positive, some studies indicate that prebiotic carbohydrates cause increased susceptibility to specific gastrointestinal infections. Here, we review existing knowledge about the impact of prebiotics on infective agents in vitro and in vivo.