Objective: In this study, the effects of radiation emitted from mobile phone (MP) on heart rate variability (HRV) which is accepted a non-invasive indicator of autonomic nervous system (ANS) were investigated with considering the deficiency of previous studies. Methods: A randomized controlled study has been designed and utilized with 30 young and healthy volunteers. During the experiment that had three periods, the electrocardiogram (ECG) and respiration signals were recorded and MP was attached to subjects’ right ear with a bone. Ten subjects selected randomly were exposed to high -level radiation during the second period (Experimental Group 1). Ten of others were exposed during the third period with maximum level radiation (Experimental Group 2). Ten records were also made while MP was closed as a control. Short -term HRV parameters were obtained and repeated measures ANOVA and suitable post-hoc tests applied to the results. Results: According to the results of the repeated measures ANOVA; there were no significant main effects of groups. However, there were some significant differences in measuring time periods and groups*period interactions. The post-hoc tests showed that mean R to R interval and HF power are significantly changed by maximum radiation emitted from MP. Conclusion: Due to the radiation emitted from MPs at maximum power, some changes may occur in HRV parameters that are associated with increased parasympathetic activity. But, the level of these changes is similar to daily activities as excitement, and stand up.