Aims: To investigate (1) differences in heart rate variability (HRV) indices between masticatory muscle pain (MMP) patients and pain-free controls at rest, during a stressor condition, and during a post-stressor recovery period, and (2) factors including psychological distress, social environment, and family-of-origin characteristics in the MMP sample compared to a pain-free matched control sample. Methods: Physiological activation and emotional reactivity were assessed in 22 MMP patients and 23 controls during baseline, stressor, and recovery periods. Physiological activity was assessed with frequency domain HRV indices. Emotional reactivity was assessed with the Emotional Assessment Scale. Analytic strategy began with overall 2 x 3 multivariate analyses of variance on physiological data followed by focused contrasts to test specific hypotheses regarding physiological and emotional status. Hypothesized differences between study groups on psychological and social-environmental variables were compared with univariate analyses of variance. Results: The MMP patients showed physiological activation during the baseline period and significantly more physiological activation during the recovery period compared to the controls. This pattern was also present in emotional reactivity between the groups. The emotional and physiological differences between the groups across study periods were more pronounced in pain patients reporting a traumatic stressor. Conclusion: These results provide further evidence of physiological activation and emotional responding in MMP patients that differentiates them from matched pain-free controls. The use of HRV indices to measure physiological functioning quantifies the degree of sympathetic and parasympathetic activation. Study results suggest the use of these HRV indices may improve understanding of the role of excitatory and inhibitory mechanisms in patients with MMP conditions. Keywords: emotional reactivity, heart rate variability, masticatory muscle pain, orofacial pain, self-regulation