Objectives : There has been a continued debate regarding the role of eye movements in Eye Movement Desensitization and Reprocessing(EMDR). This study examined the possible autonomic effect of horizontal eye movements after being exposed to fearful stimuli. Methods : Fifty two healthy adult women were randomly allocated to eye movement or eye fixed groups after watching a five minute fear-inducing film clip. ECG was recorded during the resting state, after watching the clip, and the treatment. A spectral power analysis of the heart rate variability was performed. As the variables violated the rule of normal distribution and the number in each group is small the non-parametric test was used. Results : Overall, we did not find the differences between the groups in both time and frequency domains. Some minor differences found were not consistent with results from previous studies. Conclusions : Effect of eye movement on autonomic nervous system during fear desensitization was not supported in this experiment. Further study with other psychophysiological measures is needed to understand the role of eye movements in treatment of traumatic memory.