The mechanisms by which naive helper T cells differentiate into potent cytokine-expressing effectors remain critical to understanding both successful and aberrant immune responses. Studies using Leishmania major infection of mice have revealed genetic contributions to factors that influence this differentiative process. Further, antigen recognition at the level of the T cell repertoire can also profoundly affect the outcome of disease and the appearance of discrete T cell subsets. It is likely that such mechanisms also underpin genetic susceptibility to diverse other infectious and autoimmune diseases.