The relationship between breastfeeding and allergic disease risk has been controversial. This article reviews the current evidence for the role of breastfeeding in the prevention of allergic disease. We found considerable methodological limitations inherent in most studies evaluating the effect of breastfeeding in allergic disease. Nevertheless, since randomized control trials in breast feeding research would be considered unethical, the evidence remains limited to poorer quality observational studies where participation and recall bias can severely affect the objectivity of the data collected. Furthermore, reporting of type of breastfeeding (exclusive, full or partial) may be biased by a participant's inherent belief system of what they think they should be doing. Current evidence is inconclusive regarding the effect of breastfeeding on the development of eczema, with the most recent systemic review reporting no protective effect. There is insufficient data regarding the effects of breastfeeding on objective measures of food allergy at any age. Studies show a paradoxical effect of breastfeeding on the prevention of asthma, with an apparent protective effect against early wheezing illness in the first years of life yet an increased risk of asthma in later life; however, these findings must be interpreted with caution. Existing studies fail to adequately adjust for confounders, including the critical issues of protection against early life respiratory illnesses and reverse causation. Therefore, it is possible that the effect of breastfeeding on early wheezing illness reflects protection against respiratory infection, the predominant trigger of wheezing in early childhood, rather than a true reduction in risk of asthma. In summary, future research that takes into account the potential contribution of confounding factors and effect modifiers is needed to clarify the role of breastfeeding in development of allergic disease and to inform current clinical guidelines on the prevention of allergic disease.