A genetic basis for atopic dermatitis (AD) has long-been recognized. Historic documents allude to family history of disease as a risk factor. Prior to characterization of the human genome, heritability studies combined with family-based linkage studies supported the definition of AD as a complex trait, in that interactions between genes and environmental factors and the interplay between multiple genes contribute to disease manifestation. A summary of over 100 published reports on genetic association studies through mid-2009 implicates 81 genes, 46 of which have demonstrated at least one positive association with AD. Of these, the gene encoding filaggrin (FLG) has been most consistently replicated. Most candidate gene studies to date have focused on adaptive and innate immune response genes, but there is increasing interest in skin barrier dysfunction genes. This review examines the methods that have been used to identify susceptibility genes for AD, and how the underlying pathology of this disease has been used to select candidate genes. Current challenges and the potential impact of new technologies are discussed.