The pathophysiology of atopic diseases, including asthma and allergy, is the result of complex gene-environment interactions. Since European colonization the Indigenous population of Australia has undergone significant changes with respect to their lifestyle as hunter-gatherers. These changes have had a detrimental effect on Aboriginal health, in part due to immunological modification. This review provides a comparative look at both the traditional Aboriginal/Indigenous diet and modern Western diets, examines some common allergies increasingly reported in contemporary Indigenous populations, and reviews concepts such the effect of vitamin deficiencies and changes in gut microbiota on immune function.