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Background: We investigated whether the vitamin D3 receptor gene (VDR) polymorphism can modulate therapeutic response of functional hypothalamic amenorrhea (FHA) patients to the oestroprogestagen (EP) treatment., Material and Methods: The study included 84 FHA girls and 50 controls. FHA patients underwent a four-year sequential EP therapy with 17-β oestradiol (2 mg from the 2(nd) to 25(th) day of the menstrual cycle) and didrogesterone (10 mg from the 16(th) to the 25(th) day). Their hormonal parameters were monitored along with bone turnover marker levels and bone mineral density (BMD). Additionally, the VDR gene BsmI polymorphism was determined., Results: Hormonal therapy was reflected by a substantial improvement of BMD. However, the values of BMD observed after four years of treatment in FHA patients were still significantly lower than baseline bone mineral density determined in the control group (1.007 ± 0.100 vs. 1.141 ± 0.093 g/cm(2), respectively; p < 0.001). No significant effects of the VDR genotype were observed on the dynamics of BMD during consecutive years of hormonal treatment and mean bone mineral density determined after completing the therapy (1.006 ± 0.101 vs. 1.013 ± 0.114 vs. 1.006 ± 0.094 g/cm(2) for BB, bb and Bb genotypes, respectively; p = 0.973)., Conclusions: This study did not confirm that VDR polymorphism can modulate therapeutic outcome of FHA girls subjected to the hormonal treatment. Nonetheless, this study confirmed the effectiveness of EP therapy in the simultaneous treatment of menstrual disorders and the normalisation of bone mineral density in FHA patients.