We determined the effects of 10 daily exposures of intermittent hypoxia (IH; 1 h day⁻¹; oxyhaemoglobin saturation = 80%) on muscle sympathetic nerve activity (MSNA, peroneal nerve) and the hypoxic ventilatory response (HVR) before, during and after an acute 20 min isocapnic hypoxic exposure. We also assessed the potential parallel modulation of the ventilatory and sympathetic systems following IH. Healthy young men (n= 11; 25 ± 1 years) served as subjects and pre‐ and post‐IH measures of MSNA were obtained on six subjects. The IH intervention caused HVR to significantly increase (pre‐IH = 0.30 ± 0.03; post‐IH = 0.61 ± 0.12 l min⁻¹%S⁻¹). During the 20 min hypoxic exposure sympathetic activity was significantly greater than baseline and remained above baseline after withdrawal of the hypoxic stimulus, even though oxyhaemoglobin saturation had normalized and ventilation and blood pressure had returned to baseline levels. When compared to the pre‐IH trial, burst frequency increased (P < 0.01), total MSNA trended towards higher values (P= 0.06), and there was no effect on burst amplitude (P= 0.82) during the post‐IH trial. Following IH the rise in MSNA burst frequency was strongly related to the change in HVR (r= 0.79, P < 0.05) suggesting that these sympathetic and ventilatory responses may have common central control.