The influence of discrimination on hypothalamic pituitary adrenal (HPA) axis function is considered to be more pronounced for racial minority versus majority groups, although empirical support for this argument is not strong. This study examined whether the association of perceived discrimination was more strongly associated with long-term, retrospective cortisol output (as measured by hair cortisol concentration [HCC]) among African American compared to White adults. Participants included 141 community-dwelling adults (72 White, 69 African American; mean age 45.8 years; 67% females). The Everyday Discrimination Scale assessed perceived discrimination. The first 3 cm of proximal scalp hair were analyzed for HCC using enzyme-linked immunoassay. Associations between race, perceived discrimination and HCC were examined using hierarchical multiple regression. African Americans had higher HCC than Whites, but both groups reported perceived discrimination with similar frequency. Race moderated the association between perceived discrimination and HCC (R(2) interaction = 0.03, p = 0.007) such that perceived discrimination was positively associated with HCC among African Americans (β = 0.28, p = 0.007), but not Whites (β = −0.11, p = 0.274). Perceived discrimination did not mediate the association between race and HCC (β for indirect effect = 0.025, 95% CI [−0.003, 0.087]). Although perceived discrimination did not differ between races, perceived discrimination was positively associated with retrospective levels of cortisol in scalp hair among African Americans but not Whites. This may suggest that characteristics of discrimination other than frequency are particularly salient to HPA axis function among African Americans (e.g., attribution, severity, historical context).