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Body temperatures of active lizards and their correspondence with microhabitat occupation were studied for nine species of agamid lizards in the central Australian arid zone. Thermoregulatory behaviour was also documented using several measures, such as the use of shade and perch height. The effects of thermal environment on lizard habitat occupation were hypothesized to be significant, because desert regions experience daily and seasonal extremes of temperature that are well in excess of a lizard’s preferred temperature range. All species, except Ctenophorus isolepis and Diporiphora winneckei, were found to have body temperatures that corresponded closely to ground and surface temperatures. Thermoregulatory behaviour was also found to be important throughout a lizard’s daily activity; all study species, other than Ctenophorus isolepis, were found to increase their perch height in the middle of the day. Ctenophorus isolepis was shown to be a strictly terrestrial species that uses the shade of spinifex in its thermoregulatory behaviour. Species exhibited a non-random selection of microhabitats and a preference for a particular set of thermal and structural factors. In this study, it was shown that structural factors were particularly important in microhabitat occupation. Thermal factors accounted for a smaller proportion of variance in microhabitat occupation, but still played a considerable role in the microhabitat use in central Australian agamids.