Immune dysregulation has become a hallmark of the modern era. This has led to an epidemic of disease states that result from failed immune surveillance and inappropriate or maladaptive immune responses to self-antigens (autoimmunity) and environmental antigens (allergy). Although environmental change is clearly implicated, the specific causes are still unconfirmed. Any hope to reverse such immune dysfunction must be based on a clearer understanding of the causal pathways and the environmental factors that may be driving the concerning surge in disease rates. This review explores the role of modern dietary changes that, through their known documented immune effects, may play a role in either promoting or preventing disease. Food allergen avoidance has been largely unsuccessful, and most expert bodies no longer recommend delayed complementary feeding or the avoidance of any specific allergenic foods, unless symptoms develop and allergy is confirmed. Rather, focus has shifted to other factors that may influence the ability to develop immune tolerance. There is now evidence that specific nutrients, such as folate, have the capacity to promote an allergic phenotype by epigenetically altering gene expression during early development. A number of other dietary factors including n-3 polyunsaturated fatty acids, oligosaccharides, probiotics, vitamin D, retinoic acid and other antioxidants may also clearly influence immune function and immune development. This review summarises the current evidence, recommendations and future directions in the context of allergy, with the aim of highlighting the need to further investigate the role of diet and nutrition in disease pathogenesis and prevention.