Complex autoimmune diseases are sexually dimorphic. An interplay between predisposing genetics and sex-related factors likely determines the sex discrepancy in the immune response, but conclusive evidence regarding the underlying molecular mechanisms is lacking. Using forward genetics, we positionally identified a polymorphic estrogen receptor binding site that regulates CD2 expression, leading to female-specific differences in mouse models of T cell-dependent autoimmunity. Female mice with reduced CD2 levels displayed a diminished T cell activation and autoimmune T cell response. Mechanistically, CD2 affected LAG-3 expression. Our findings help to explain the sexual dimorphism in human autoimmunity, as CD2 associated with rheumatoid arthritis and its regulation through 17-β-estradiol was conserved in human T cells. Hormonal regulation of CD2 has implications for CD2-targeted therapy. Indeed, anti-CD2 treatment more potently affected female mice. In conclusion, our results demonstrate the relevance of sex-genotype interactions and deliver strong evidence for CD2 as a sex-sensitive predisposing factor in autoimmunity.