Patients with a higher BMI (aOR 0.87, 95% CI 0.84–0.91, P < 0.001) and AMH value (aOR 0.97, 95% CI 0.95–0.99, P = 0.007) were less susceptible to ovarian cysts after GnRH agonist supplementation, whereas a higher basal E2 level increased their incidence (aOR 1.01, 95% CI 1.00–1.01, P = 0.002). This evidence concerns the gene GNRH1 and Ovarian cyst.