Exposure to alien inter-group environments can differently effect ethnic groups\' autonomous nervous system, measured by heart rate variability (HRV). Our aim was to evaluate the effect of crossing alien ethnic boundaries on heart rate variability in three selected types of environments. In a field experiment study, we test responses of 72 Muslim and Jewish women to exposure to alien ethnic environments. We measured their HRV in intra and inter-ethnic parks, town centers and residential neighborhoods in Arab and Jewish adjacent towns. The subjects stayed half an hour in each environment. Mixed models were used to evaluate the effects. The results show that for both groups more favorable HRV measurements were demonstrated in intra-ethnic environments as compared to their HRV once crossing ethnic boundaries. The strongest effect in frequency domain (LF/HF) in response to ethnic boundary crossing was observed in the park for Muslims (beta:0.65, 95%CI: 0.60-0.70) and for Jews (beta: 0.60, 95%CI: 0.57-0.63). Following the eruption of the uprising, the most significant increase in LF/HF in response to ethnic boundary crossing was demonstrated in parks (beta: 0.66, 95%CI: 0.60-0.71). In conclusion, both groups are effected by boundary crossing but there are ethnic differences in the autonomic nervous system balance and in response to crossing alien ethnic boundaries. A further study is needed to understand the causes of these differences.