Stress levels in organisms provide a rapid measure for assessing population health. Handling and capture stress, however, cause error in blood measures, so this method is rapidly being replaced by assessing levels of stress metabolites in faeces. This eliminates the source of error because there is a lag period between stress perception and the resultant stress metabolite accumulation within faeces. This lag period is correlated with specific intestinal passage time, a measure that can vary greatly between taxa, particularly amongst ectotherms. Due to two deleterious consequences associated with extended exposure of the metabolites to the intestinal environment, species that exhibit long and variable intestinal passage times are not good candidates for metabolite studies. We measured gut and intestinal passage times in Trachylepis margaritifer to ascertain whether it would be an appropriate candidate for stress metabolite studies. We first tested if barium sulphate in the meal had an effect on gut passage time at three ambient temperatures (25, 27 and 32 °C). Barium sulphate had no effect; however, temperature had a significant effect with an unexpected pattern: gut passage time was fastest at 32 °C but was slower at 27 °C than at 25 °C. We then used X-ray technology and barium sulphate-loaded meals to measure gut and intestinal passage times at 25 and 27 °C. This allowed us to observe which parts of the digestive process were responsible for increased passage times at 27 °C: the faster passage time at 25 °C was due to faster intestinal passage time; there was no difference in gastric emptying time. We assess the species to be a suitable candidate for studies using faeces to measure stress. It is imperative however, that the effect of temperature on passage rates is known and taken into account in such studies.