While the effects of instantaneous, single-bout exposure to hypoxia have been well researched, little is known about the autonomic response during, or as an adaptation to, repeated intermittent hypoxic exposure (IHE) in a sedentary population. Resting heart rate variability (HRV) and exercise capacity was assessed in 16 participants (8 receiving IHE, [Hyp] and 8 receiving a placebo treatment [C]) before and after a 4-week IHE intervention. Heart rate variability was also measured during an IHE session in the last week of the intervention. Post-intervention, the root mean squared successive difference (rMSSD) increased substantially in Hyp (71.6 +/- 52.5%, mean change +/- 90% confidence limits) compared to C suggesting an increase in vagal outflow. However, aside from a likely decrease in submaximal exercise heart rate in the Hyp group (-5.0 +/- 6.4%) there was little evidence of improved exercise capacity. During the week 4 IHE measurement, HRV decreased during the hypoxic exposure (reduced R-R interval: -7.5 +/- 3.2%; and rMSSD: -24.7 +/- 17.3%) suggesting a decrease in the relative contribution of vagal activity. In summary, while 4 weeks of IHE is unlikely to improve maximal exercise capacity, it may be a useful means of increasing HRV in people unable to exercise.