Alopecia areata is a complex, non-scarring hair loss disease that affects approximately 1-2% of the population. The etiology of AA is unknown, although both genetic factors and environmental agents are thought to contribute to the immune disregulation leading to the final pathways of disease. Here, we examine the complex interplay of genetic and non-genetic factors that, no doubt, underpin the wide-ranging clinical expression of AA. We further discuss emerging strategies and tools that promise to better define the genetic basis of disease and reveal novel targets for next generation therapies.