Over the past few decades, the rise in the prevalence of allergic conditions has been notable. The literature suggests an association between the human microbiota and the development of allergic conditions such as asthma and atopic dermatitis. Patients with atopy exhibit alterations in the relative levels of ‘beneficial’ and potentially harmful bacteria compared to healthy controls. One proposed mechanism is that changes in gut microbiome composition and function, which are altered by various environmental exposures, influence the healthy development of the immune system and thereby affect immune tolerance. Specific species of commensal bacteria and their functions as well as biologically active metabolites may play either a protective or a pathogenic role in the development of allergy or asthma. This article aims to summarise briefly the human gut, skin and respiratory microbiome and the link to allergic conditions as well as to consider the African data.