Analysis of heart rate variability (HRV) is increasingly applied in research and intervention. However, the sensitivity of the variety of HRV parameters for changes in cardiovascular reactivity remains unclear. This study investigated effect sizes of HRV parameters in an experimental field study, exposing persons to 2700 m altitude. Parameters analyzed were mean heart rate (HR), atrioventricular conduction time, SDNNi, rMSSD, pNN50, pNNxx (xx = pNN05, pNN10, pNN20, pNN25, pNN30, pNN40), LF, HF, LFnu, LF/HF ratio, and Total Power, as well as ratings of arousal and mood. Forty-five persons were taken to the Dachstein mountain by cable car. HRV parameters of 40 min epochs and ratings at 170 m and 2700 m were compared. At altitude, HR increased and HRV decreased in all parameters. Although moods were not changed, test persons experienced higher arousal at altitude. Besides for HR, analysis revealed the highest effect size for SDNNi, followed by pNN20 and pNN25 and was much lower for HF. As pNNxx parameters were highly correlated with HF, they are discussed to reflect vagal activity. Moreover, pNNxx parameters are clearly defined, whereas HF is susceptible to variations in computation; thus pNNxx parameters seem preferable due to higher effect sizes and better comparability.