Chronic neck pain (CNP) and chronic low back pain (CLBP) are prevalent musculoskeletal disorders linked to autonomic nervous system dysfunction, assessed through heart rate variability (HRV). This study aimed to compare HRV indices among subjects with CNP, CLBP, and healthy controls, examining whether pain location influences autonomic modulation. An observational study was conducted involving 93 adults (31 per group: CNP, CLBP, and controls). HRV was measured using a Firstbeat Bodyguard® device, analyzing parameters including mean HR, minimum and maximum HR, rMSSD, SD1, SD2, stress score (SS), and sympathetic/parasympathetic ratio (S:PS). HRV data were analyzed following standard guidelines. Additional analyses included multinomial logistic regression and ROC curves to explore the predictive value of rMSSD. Both pain groups showed significantly higher sympathetic dominance (higher SS and S:PS ratio) compared to controls (p < 0.001, d = 1.0-1.3). Subjects with CNP exhibited significantly lower parasympathetic indices (rMSSD and SD1) compared to the CLBP group (both p < 0.01, d = 0.8) and healthy controls (p < 0.001, d = 2.2 and d = 2.3). No differences were observed in sympathetic dominance between CNP and CLBP groups. Logistic regression confirmed the predictive value of rMSSD for group classification, and ROC analyses showed high discriminatory capacity, particularly between CNP and healthy subjects (AUC = 0.932). Significant differences in autonomic modulation were observed between patients with CNP, CLBP, and healthy subjects. CNP was associated with a greater reduction in parasympathetic activity, possibly due to mechanisms related to the anatomical proximity of the vagus nerve to the cervical region.
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