Background: Patients with chronic musculoskeletal pain have a higher chance of presenting impairment in cardiovascular autonomic modulation, which may have implications for cardiovascular events. The autonomic nervous system plays an important role in pain modulation. However, it is unclear whether patients with inefficient descending nociceptive inhibition have poorer cardiovascular autonomic modulation. Objective: To compare the cardiovascular autonomic modulation of patients with musculoskeletal pain who had normal versus impaired functioning of descending nociceptive inhibitory system (DNIS). Study Design: A cross-sectional study. Setting: Physiotherapy outpatient service. Methods: Fifty-six patients with musculoskeletal pain were included. Conditioned pain modulation was assessed by the difference of algometric values held in the dorsal forearm and tibialis anterior muscle, before and after a thermal pain stimulus was employed via the cold pressure test (CPT). Patients with inefficient DNIS in both sites were classified as impaired responders (n = 14). The others were classified as normal responders (n = 42). Cardiac autonomic modulation was monitored at rest by heart rate variability (HRV). The blood pressure response to the CPT was used as a proxy of sympathetic responsiveness. Results: Most of the patients were women (60%) and had chronic pain (75%). The groups had similar demographic characteristics. Patients with impaired DNIS showed lower HRV [RMSSD (P = 0.020), SDRR (P = 0.009), HF (ms2 ) (P = 0.027), LF (ms2 ) (P = 0.004), and total power (P = 0.002)]. The blood pressure response to CPT was similar between groups (systolic pressure, P = 0.813; diastolic pressure, P = 0.709). Limitation: Physical activity level, emotional changes, and visceral pathologies can alter the autonomic nervous system and may represent potential confounders. The low number of patients may have biased the results. Conclusion: Patients with impaired DNIS presented lower resting HRV, indicating an altered vagal control of the heart. In contrast, the blood pressure response to a sympathoexcitatory stimulus was preserved. The study was approved by the Research Ethics Committee of Augusto Motta University Centre (CAAE number: 46245215.9.0000.5235), and all patients signed the Informed Consent Form. Key words: Musculoskeletal pain, autonomic nervous system, heart rate, chronic pain, diffuse noxious inhibitory control, blood pressure, sympathetic nervous system, parasympathetic nervous system