The afferent branch of the autonomic nervous system contributes with interoception to the multimodal sensory correlation continuously needed to update our representation of the body. To test whether the modulation of body representation would have an impact on the efferent branch of the autonomic nervous system, nonspecific skin conductance has been measured in three rubber hand illusion (RHI) experiments, controlled with asynchronous brush-stroking and incongruent fake hand position. Nonspecific skin conductance standard deviation (SCSD) computed along the whole 90 sec of stroking was found to be increased by the illusion and to correlate with all the typical measures of embodiment. Computing SCSD in shorter time windows strongly enhanced the difference between illusion and controls. The highest difference was found in the 10–55 sec window, being the 14–34 sec window as the most informative one. The higher correlations with the validated measures of embodiment (all but the proprioceptive drift) were found for time windows ranging between 35 and 65 sec. The SCSD was no longer significantly higher when the RHI was repeated twice (two trials each iteration), but it was still significantly higher in synchronous stroking even when considering only the second trial. However, after the first iteration of the RHI paradigm, the effect of the embodiment on nonspecific skin conductance response results to be attenuated, suggesting that novelty in presentation of the RHI can contribute to the effect on nonspecific skin conductance response. Results candidate SCSD as a noninvasive, cheap, easy, and objective measure of embodiment, especially sensible to onset and strength of the illusion. Alike the already known enhanced autonomic reaction to a threatening, SCSD does not interfere with the collection of other behavioral measures. Correlations and their dynamics, presence of the effect in the second presentation of the setup but relative low robustness against multiple repetition, suggest that the increased fluctuations of skin conductance caught by SCSD are not just the effect of different presented sensory stimuli but more likely a stronger arousal response to the novelty of the updated perceptual status.