Reduced bone mineral density (BMD) is present in many women with Turner syndrome (TS), and hypo-estrogenism is known to play a vital role in bone mineralization disturbances. It has been suggested that genetic factors play an important role in the regulation of BMD. The aim of this study was to analyze the association between Pvu II and XbaI ER-α polymorphisms and BMD in TS patients subjected to estroprogestagen (EP) treatment. Thirty-two TS patients aged 17-38 (mean age 22.7 ± 8.2) along with 82 healthy controls were the subjects for this study. Baseline values of hormonal parameters, BMD and bone density markers were measured in the subjects. Subsequently, TS patients underwent 4 years of EP therapy. The results of laboratory parameters and BMD were analyzed in regard to PvuII and XbaI polymorphic variants of the ER-α gene. The increase in BMD of TS subjects was the highest in the 1st (7.5%, p = 0.013) and 2nd (6.6%, p = 0.008) years of treatment. Four years of EP therapy was reflected by a significant increase in BMD z-scores in patients with xx and Xx genotypes of the XbaI gene and in those with with the pp and Pp genotypes of PvuII. In patients with haplotypes other than XXPP, BMD z-scores were significantly higher compared to their baseline after 2 (p = 0.002), 3 (p < 0.001) and 4 (p < 0.001) years of treatment. In conclusion, genotypes xx and pp were shown to be prognostic markers of a good response to EP treatment, whereas the XXPP haplotype carriers were revealed to have the risk factors for insufficient responsiveness against EP treatment in BMD control.