The age-related decline in fat-free mass is accelerated in women after menopause. The role of ovarian hormone deficiency in the regulation of fat-free mass, however, has not been clearly defined. To address this question, we examined the effect of ovarian hormone suppression on whole body protein metabolism. Whole body protein breakdown, oxidation and synthesis were measured using [¹³C]leucine in young, healthy women with regular menstrual patterns before and after two months of treatment with gonadotropin-releasing hormone agonist (GnRHa; n=6) or placebo (n=7). Protein metabolism was measured under postabsorptive and euglycemic-hyperinsulinemic-hyperaminoacidemic conditions. Ovarian suppression did not alter whole body or regional fat-free mass or adiposity. In the postabsorptive state, GnRHa administration was associated with reductions in protein breakdown and synthesis (P<0.05); whereas, no change in protein oxidation was noted. Under euglycemic-hyperinsulinemic-hyperaminoacidemic conditions, a similar reduction (P<0.05) in protein synthesis and breakdown was noted; whereas, protein oxidation increased (P<0.05) in the placebo group. Testosterone, steroid hormone precursors, insulin-like growth factor-I and their respective binding proteins were not altered by GnRHa administration and changes in these hormones over time were not associated with GnRHa-induced alterations in protein metabolism, suggesting that changes in protein turnover are not due to an effect of ovarian suppression on other endocrine systems. Our findings provide evidence that endogenous ovarian hormones participate in the regulation of protein turnover in women.