Systemic lupus erythematosus is a chronic, multisystem, inflammatory autoimmune disease of unknown origin characterized by the production of nonorgan-specific auto-antibodies and a broad spectrum of clinical and immunological manifestations. This study was conducted to assess the association of cytochrome P450 polymorphism with ovarian toxicity and clinical response in patients with systemic lupus erythematosus treated with intravenous pulse cyclophosphamide. Forty seven SLE patients and twenty control subjects were included in this study. The association between cytochrome P450 (CYP2C19) genotypes and the incidence of ovarian toxicity in SLE patients was significant. Also, the association between cytochrome P450 genotypes of SLE patients and their hormonal levels was highly significant.