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The aim of this study was to assess the dynamical interaction between the cardiovascular autonomic control and sex hormones in perimenopausal women under menopausal hormone therapy (MHT).Seventy women (age: 51.6±2.1 years) were treated with MHT. Standard time and frequency domain measures of heart rate variability (HRV) and index S of synchronization between the slow oscillations in HRV and photoplethysmographic waveform variability were studied during a 6-week treatment with MHT. We assessed also the dynamics of the following sex hormones: estradiol, follicle-stimulating hormone, dehydroepiandrosterone sulfate, and testosterone.MHT increased estradiol and decreased follicle-stimulating hormone. Hot flashes and index S were significantly decreased under MHT (P<0.05). Other autonomic indices were not significantly changed (P>0.05). Changes of index S did not correlate with changes of sex hormones and hot flushes (P>0.05).The obtained results may indicate the independence of heart autonomic control (assessed by HRV measures) from women’s hormonal status. However, any changes in sex hormones contribute to changes in the systemic control of circulation, which is assessed by index S.