Besides pre- and pro-biotic-containing infant formulae, fermented infant formulae are commonly used to relieve or prevent symptoms of gastrointestinal (GI) discomfort in young infants. During the fermentation process in cow's milk-based formulae, the beneficial bacteria modulate the product by forming several beneficial compounds, which contribute to the alleviation of the symptoms observed. This review summarizes the clinical evidence on the impact of fermented infant formulae on common pediatric GI-symptoms. The potential mechanisms involved are discussed: i.e., the lactose and protein (in-) digestibility, effects on gastric emptying and gut transit and modulation of the colonic microbiota. Although initial evidence indicates a beneficial effect of fermented formulae on GI discomfort in newborns, validation and confirmation of the clinical proof obtained so far is warranted, as well as further research to (more fully) understand the mode of action.