Objective: To compare hormonal and clinical responses to GnRH pulsatile treatment in weight-recovered anorexia nervosa patients (Rec-AN) with persistent functional hypothalamic amenorrhea (HA) vs. in patients with secondary and primary HA. Design: Retrospective, observational, ambulatory study. Setting: University hospital. Patient(s): Forty-one women: 19 Rec-AN (body mass index >18.5 kg/m(2) without menses recovery), 15 secondary HA without any eating disorders patients (SHA), and 7 primary HA patients (PHA). Intervention(s): Gonadotropin-releasing hormone pulsatile therapy. Main Outcome Measure(s): Baseline E-2, LH, and P plasma levels and their changes during induction cycles; ovulation, follicular recruitment, and pregnancies. Results: The Rec-AN group displayed higher basal E-2 and LH plasma levels after GnRH injection compared with SHA and PHA. Higher E-2 and LH levels were observed during induction cycles in Rec-AN compared with SHA and PHA. Follicular recruitment was higher in Rec-AN. The ovulation rate was higher in Rec-AN compared with PHA but similar to SHA. Conclusion(s): This study showed increased gonadal status and higher E-2 response to pulsatile GnRH therapy in persistent amenorrheic weight-recovered AN compared with HA from other causes. It suggests that their individual set-point of body weight allowing a fully functional gonadal axis is not reached yet. Specific factors of gonadal inertia in Rec-AN still remain unclear.