Duration and start time of respirometry experiments have significant effects on the measurement of basal values for several commonly measured physiological variables (metabolic rate, evaporative water loss and body temperature). A longer measurement duration reduced values for all variables for all start times, and this was an effect of reduced animal activity rather than random sampling. However, there was also an effect of circadian rhythm on the timing of minimal physiological values. Experiment start time had a significant effect on time taken to reach minimal values for all variables, ranging from 0400 hours ± 38 min (body temperature, start time 2300 hours) to 0854 hours ± 52 min (evaporative water loss, start time 1700 hours). It also influenced the time of day that minimal values were obtained, ranging from 2224 hours ± 40 min (carbon dioxide production, start time 1500 hours) to 0600 hours ± 57 min (oxygen consumption, start time 2300 hours), and the minimum values measured. Consequently, both the measurement duration and the experiment start time should be considered in experimental design to account for both a handling and a circadian effect on the animal's physiology. We suggest that experiments to measure standard physiological variables for small diurnal birds should commence between 1700 and 2100 hours, and measurement duration should be at least 9 h.