Background: Alexithymia, the inability to describe one's own emotions, is linked to deficits in empathy, manifesting as a diminished capacity to recognize or understand the emotions and mental states of others. Several brain centers of autonomic control and interoception that are activated in empathy are thought to misfunction in alexithymia. We hypothesized that individual differences in autonomic changes under affective stimulation might be associated with differences in alexithymia and empathy. Methods: We studied 21 healthy volunteers, comparing their alexithymia and empathy scores with changes in their sympathetic autonomic arousal, indexed by the palmar skin potential level, during 3 tasks: playing a computer game, performing mental arithmetic, and watching a negative emotional valence video. Results: Both autonomic and subjective sense of arousal increased at the beginning of each task and then gradually subsided over the course of the task. Higher autonomic arousal at the onset of the computer game was associated with higher empathy scores, and at the onset of the negative video with higher scores for both empathy and alexithymia. Alexithymia delayed the habituation of autonomic arousal during the computer game, while the empathy score was related to a faster decline in arousal during the negative video task. Conclusions: High alexithymia and high empathy scores were linked to increased autonomic arousal at the onset of emotional stimulation, but were distinguishable in the rates of habituation of the evoked arousal. Our data provide insight into the relationships among interacting psychological traits, physiologic regulation, and the arousal dimension of emotional experience.