The decrease in body temperature (T(b)) observed in most vertebrate classes in response to hypoxia has been attributed to a regulated decrease in set-point, protecting organs against tissue death due to oxygen depletion. Hypoxia, however, imparts particular challenges to metabolic function which may, in turn, affect thermoregulation. In ectotherms, where thermoregulation is mainly behavioural, stressors that influence the propensity to move and respond to temperature gradients are expected to have an impact on thermoregulatory control. Using low oxygen as a potent stressor, we evaluated the variability and level of thermoregulation of inland bearded dragons. To examine the source of thermoregulatory variability, we studied their behaviour in an electronically controlled temperature-choice shuttle box, a constant temperature dual-choice shuttle box, and a linear thermal gradient. A significant increase in the size of the T(b) range was observed at the lowest oxygen concentration (4% O(2)), reflecting a decrease in thermoregulatory precision in the temperature-choice shuttle box. This was also accompanied by a drop of approximately 2-4 degrees C in T(b), the drop being greatest in situations where T(b) must be actively defended. Situations that force the lizards to continually choose temperatures, rather than passively remain at a given temperature, lead to an increase in the variability in the manifested T(b), which is further exaggerated in hypoxia. This study reveals that a decrease in thermoregulatory precision caused by a diminished propensity to move or effect appropriate thermoregulatory responses may be a contributing component in the lowering of selected body temperatures observed in many hypoxic ectotherms.