Background/Aims: To investigate the etiology of hypogonadism in women with Prader-Willi Syndrome (PWS). Methods: Ten women aged 23 ± 5.5 years with PWS and 10 age- and BMI-matched controls were included. Blood samples were drawn and abdominal ultrasounds were performed on days 2–4 of spontaneous cycles or at random from amenorrheic women. Anti-Müllerian hormone (AMH), inhibin B (INB), gonadotropins, sex steroids, TSH, prolactin, ovarian volume and antral follicle count (AFC) in PWS women were compared with results from controls and the reference ranges. Results: Compared to controls, PWS women had lower INB (mean ± SD = 17.6 ± 12.8 pg/ml vs. 110.6 ± 54.5; p = 0.0002) and AMH levels (1.18 ± 0.86 ng/ml vs. 3.53 ± 2.42; p = 0.01). INB levels were exceptionally low in all PWS women, but individual AMH levels overlapped with the levels in the controls. Ovarian volume (mean ± SD = 3.7 ± 2.3 ml vs. 30.5 ± 28.8; p = 0.03) and AFC (6.4 ± 6.9 vs. 14.0 ± 8.2; p = 0.01) were lower in the PWS group compared to the controls. Three PWS patients had abnormally high follicle-stimulating hormone levels, while only 1 had hypogonadotropic hypogonadism. Conclusions: Our results suggest a unique follicular stage-specific insult in women with PWS. Thus, primary ovarian dysfunction is a major component of hypogonadism in PWS.

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