Knowing the output of the "body clock" is fundamental to the science of chronobiology. As the clock resides within the suprachiasmatic nuclei, direct measurement is not feasible and therefore, characteristics of the clock are often inferred from the measurement of marker rhythms, one of which is core temperature. Core temperature is often the marker rhythm of choice due to ease of measurement, particularly in field conditions. However, if the output of the "body clock" is to be inferred from measurement of this variable, it is important to establish whether environmental conditions change or moderate the circadian rhythm of core temperature. Although the majority of circadian patterns do demonstrate independence from such exogenous influences, there does appear to be seasonal variation to their period. Given that humans can easily travel to environments of altered temperature and altitude, there is a need to ascertain the exact effect of such change on the rhythm of core temperature. This review will therefore outline the evidence that the circadian rhythm of core temperature is affected by ambient temperature and by hypoxia. Furthermore, the review will discuss whether these environmental factors act as zeitgebers (affecting the endogenous rhythm) or as masking influences of the inherent rhythm.