Following exposure to intermittent hypoxia respiratory motor activity and sympathetic nervous system activity may persist above baseline levels for over an hour. The present investigation was designed to determine whether sustained increases in minute ventilation and sympathovagal (S/V) balance, in addition to sustained depression of parasympathetic nervous system activity (PNSA), were greater in males compared to females following exposure to intermittent hypoxia. Fifteen healthy males and females matched for age, race and body mass index were exposed to 8 – 4 minute episodes of hypoxia during sustained hypercapnia followed by a 15 minute end recovery period. The magnitude of the sustained increase in minute ventilation during the end-recovery period, compared to baseline, was similar in males and females (males - 1.52 ± 0.03; females - 1.57 ± 0.02 fraction of baseline; p < 0.0001). In contrast, depression of PNSA and increases in S/V were evident during the end recovery period, compared to baseline, in males (PNSA - 0.66 ± 0.06 fraction of baseline, p < 0.0001; S/V - 2.8 ± 0.7 fraction of baseline, p < 0.03) but not in females (PNSA - 1.27 ± 0.19 fraction of baseline, p = 0.3; S/V balance - 1.8 ± 0.6 fraction of baseline, p = 0.2). We conclude that a sustained increase in minute ventilation is evident in both males and females following exposure to intermittent hypoxia and that this response is independent of gender. In contrast, sustained alterations in autonomic nervous system activity were evident in males but not in females.