The safety and quality of infant milk, whether it is breast milk (BM) or infant formula (IF), are a major concern for parents and public health authorities. BM is recommended as the gold standard at WHO level. However, nowadays IF appears as an essential alternative in Western countries, challenging producers to optimise nutritional quality and safety of IF. The aim of the present paper is to give an overview on the assessment and comparison of risks and benefits associated with BM and IF consumption. To date, this intensively debated subject has been mainly investigated. It has been shown that both diets could be sources of beneficial health effects in terms of nutrition and also risks in terms of chemical safety. Moreover, microbiologists have demonstrated that IF consumption can cause illness due to product contamination or inappropriate milk preparation. The paper concludes on the bottlenecks and gaps which should be investigated to further progress the quantification of the impact of early diet on infant health. Performing a multi-disciplinary risk-benefit assessment with DALY as endpoint, might be a future option to help prioritise management options.