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The pain was quantified by assessing the pressure pain threshold (PPT<\/jats:styled-content>), VAS<\/jats:styled-content> of pain, and the pain component of the SF<\/jats:styled-content>\u201036 questionnaire. The RR<\/jats:styled-content> intervals were recorded in the supine position and during the DBT<\/jats:styled-content>. The heart rate variability (VHR<\/jats:styled-content>) was measured by methods in the time and frequency domain.<\/jats:p><\/jats:sec>Results<\/jats:title>The group with FMS<\/jats:styled-content> had abnormal cardiac autonomic modulation at rest and during DBT<\/jats:styled-content>, compared to CG<\/jats:styled-content> (P<\/jats:italic>\u00a0<\u00a00.05). Positive correlations were found between PPT<\/jats:styled-content> and the E\/I ratio (r<\/jats:italic>\u00a0=\u00a00.70), \u0394FC<\/jats:styled-content> (r<\/jats:italic>\u00a0=\u00a00.66) and power spectrum density (DEP<\/jats:styled-content>, r<\/jats:italic>\u00a0=\u00a00.56) indices of DBT<\/jats:styled-content>, as well as between pain component of the SF<\/jats:styled-content>\u201036 and the E\/I ratio (r<\/jats:italic>\u00a0=\u00a00.49), \u0394FC<\/jats:styled-content> (r<\/jats:italic>\u00a0=\u00a00.45) and DEP<\/jats:styled-content> (r<\/jats:italic>\u00a0=\u00a00.50) indices of DBT<\/jats:styled-content>. Significant correlations were observed between the FIQ<\/jats:styled-content> questionnaire and the LF<\/jats:styled-content>\/HF<\/jats:styled-content> ratio index in the supine position and the E\/I ratio (r<\/jats:italic>\u00a0=\u00a0\u22120.63), \u0394FC<\/jats:styled-content> (r<\/jats:italic>\u00a0=\u00a0\u22120.54), and DEP<\/jats:styled-content> (r<\/jats:italic>\u00a0=\u00a0\u22120.51) indices of DBT<\/jats:styled-content>.<\/jats:p><\/jats:sec>Conclusions<\/jats:title>The results of VHR<\/jats:styled-content> indices during the supine position and the DBT<\/jats:styled-content> women with FMS<\/jats:styled-content> suggest impairment of neurocardiac integrity associated with pain and the impact of FMS<\/jats:styled-content> on the quality of 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