In mammals, biological time keeping is organised with a hierarchical and pyramidal structure, under the control of the master clock in the suprachiasmatic hypothalamic nuclei (SCN). Body temperature (Tb) and metabolic rate have robust circadian patterns, and probably represent primary variables controlled closely by the SCN. From the data of studies in animals (mostly rats) and humans, it appears that the most common effect of prolonged hypoxia is to decrease, and in some cases to abolish, the amplitudes of the daily oscillations, irrespective of the state of arousal or activity level. On the other hand, the evidence is that hypoxia causes only minimal and transient perturbation of the period of the rhythm. The fact that hypoxia modifies the circadian oscillations of variables as important as body temperature and metabolism leads to the expectation that the daily rhythms of many other functions are perturbed by hypoxia, according to their link to the primary variables. The data currently available, although sparse and fragmentary, support this view. It is speculated that the alterations of the normal circadian oscillations can contribute to many common symptoms during sustained hypoxia, from sleep fragmentation, to malaise and loss of appetite.