In 2011, the Committee on Nutrition of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition systematically reviewed published evidence related to the safety and health effects of the administration of formulae supplemented with pro- and/or prebiotics compared with unsupplemented formulae. We updated evidence on the effects of the administration of prebiotic-supplemented infant formulae (IF) compared with unsupplemented IF. Five databases were searched up to March 2017 for randomised controlled trials. In all, forty-one publications were identified, including twenty-five new publications. The administration of currently evaluated prebiotic-supplemented formulae to healthy infants does not raise safety concerns with regard to growth and adverse effects. Some favourable clinical effects are possible, primarily stool softening, which may be beneficial in some infants. Currently, there is no existing robust evidence to recommend the routine use of prebiotic-supplemented formulae. The latter conclusion may reflect the small amount of data on specific prebiotics and outcomes, rather than a genuine lack of an effect. The efficacy and safety should be considered for each prebiotic(s)-supplemented formula.