Background and objectives: The gut microbiome has been associated with a wide range of chronic diseases including obesity, diabetes and cardiovascular disease, inflammatory and neurological diseases. Early colonisation of the infant gut may be key to the development of gut microbiome in later life but our understanding of the factors which determine the colonisation process and how that links to later/adult health is still incomplete. Many studies have suggested that the human milk microbiome contributes significantly but it is unclear how the bacteria detected in breastmilk are derived and if they survive in the infant gut. We explored the evidence in a systematic review. Methods: A systematic review was carried out to answer ‘What evidence exists with regards to early colonization of the infant gut by bacteria coming from breast milk?’ Search terms included: ((“Microbiota”[Mesh] OR “Metagenome”[Mesh] OR “Dysbiosis”[Mesh]) AND “Anti-Bacterial Agents”[Mesh]) AND (“Infant”[Mesh] OR “Infant, Extremely Premature”[Mesh] OR “Infant, Extremely Low Birth Weight”[Mesh] OR “Infant, Low Birth Weight”[Mesh] OR “Infant, Very Low Birth Weight”[Mesh] OR “Infant, Small for Gestational Age”[Mesh] OR “Infant, Premature”[Mesh] OR “Infant, Postmature”[Mesh] OR “Infant, Newborn”[Mesh] OR “Infant, Premature, Diseases”[Mesh])and (microbiota OR bacteria OR microflora OR microbes) AND (dysbiosis) AND (infant OR neonate OR baby) AND (health) AND (disease) AND (birth OR parturition) AND (breastmilk OR breast milk OR human milk) AND (breastfeeding OR breast feeding OR breastfed) AND (formula fed OR infant formula OR bottle fed OR bottle feed) AND (lactation). Searches were carried out using PUBMED, OVID, LILACS and PROQUEST. Results: After initial removal of duplicates and not-relevant papers, 66 papers remained for detailed review. This was carried out independently by three authors before final evaluation of the evidence. Papers were considered for information on sample collection, avoidance of contamination procedures, specified bacterial analysis methods and kits used, and if they discussed maternal and infant events that may influence colonisation including mastitis and antibiotic use. Conclusions: Many studies reported a range of different bacteria in breastmilk. There remains a need to understand the breastmilk microbiome and the modifiable factors which influence this to support health promoting microbial development in the offspring.