Objective To examine health, psychological, and autonomic impairment differences between individuals with fibromyalgia and those with other chronic benign pain in these conditions. The possible role of the autonomic nervous system in the maintenance of chronic benign pain can be examined using heart rate variability (HRV), which measures the interplay between the excitatory sympathetic and the inhibitory parasympathetic nervous system. Predictors of HRV will also be examined. Methods This study examined resting HRV in a sample of 84 patients with chronic benign pain, a subgroup of whom had fibromyalgia. Participants completed a battery of self-report measures and underwent measurements of resting HRV. Results Individuals with fibromyalgia experienced higher levels of depression (t (82)=−2.27, p <.05) and significantly greater difficulty with physical functioning (t (75.8)=2.65, p <.01) than did those with other chronic benign pain, there were no significant differences in any of the HRV indices. Across all pain conditions, we found that age, gender, physical health functioning, pain anxiety, and pain sensations were all significant predictors of HRV, suggesting that each are involved in the relationship between chronic benign pain and autonomic function. Conclusions These findings emphasize the importance of addressing psychological distress and physical functioning in chronic pain populations and specifically fibromyalgia. Future research can further examine the role of physical health functioning, psychological distress, and pain severity in the relationship between chronic pain and autonomic abnormalities.