OBJECTIVE: To quantify autonomic dysfunction in fibromyalgia patients compared to healthy controls using heart rate variability (HRV). METHODS: Sixteen patients with fibromyalgia and 16 healthy controls were recruited in this case control study. HRV was measured using the time-domain method incorporating the following parameters: total heartbeats, the mean of intervals between consecutive heartbeats (R-R intervals), the standard deviation of normal to normal R-R intervals (SDNN), the square root of the mean squared differences of successive R-R intervals (RMSSD), ratio of SDNN to RMSSD (SDNN/RMSSD), and difference between the longest and shortest R-R interval under different three conditions including normal quiet breathing, rate controlled breathing, and Valsalva maneuver. The severity of autonomic symptoms in the group of patients with fibromyalgia was measured by Composite Autonomic Symptom Scale 31 (COMPASS 31). Then we analyzed the difference between the fibromyalgia and control groups and the correlation between the COMPASS 31 and aforementioned HRV parameters in the study groups. RESULTS: Patients with fibromyalgia had significantly higher SDNN/RMSSD values under both normal quiet breathing and rate controlled breathing compared to controls. Differences between the longest and shortest R-R interval under Valsalva maneuver were also significantly lower in patients with fibromyalgia than in controls. COMPASS 31 score was negatively correlated with SDNN/RMSSD values under rate controlled breathing. CONCLUSION: SDNN/RMSSD is a valuable parameter for autonomic nervous system function and can be used to quantify subjective autonomic symptoms in patients with fibromyalgia.