The increase in the prevalence of atopic diseases in the developed world is becoming an increasing problem. Exclusive breastfeeding in early life has been associated with a reduction of incidence of atopic disorders, largely because breastmilk has the ability to shape the composition of the infant gut microbiome and the development of the immune system. The mother's breastmilk transmits elements of her own microbiome and immune responses, and also provides specific prebiotics to support growth of beneficial bacteria. It is important to evaluate the role of genetic, environmental and lifestyle factors that contribute to disease development. Exposure to allergens through a disrupted skin barrier in combination with nutritional factors in individuals with a genetic predisposition may lead to the development of allergic diseases. Early environmental, microbial and dietary exposures may influence the development of the immune system by epigenetic mechanisms. The ability of the microbiome to act as an epigenetic modulator has been recently demonstrated by the observation of epigenetic DNA modifications after exposure to microbial antigens in immature human cells from intestinal epithelia. The interactions between early nutrition, microbiome and the epigenome during the early phases of human development are very complex and incompletely understood. Better elucidation of the protective bioactive components of breastmilk and the impact of intestinal microbial composition on the epigenome could lead to new targets for the treatment and prevention of allergic disease.