The purpose of the present study was to examine the discrepancies in rectal temperature (T (re)) at various depths. Nineteen young males performed two bouts of bicycle exercise and recovery. T (re) was simultaneously measured at depth of 4, 6, 8, 10, 13, 16, and 19 cm, alongside the measurement of skin temperatures. We found small but statistically significant differences by depth in the absolute T (re), the magnitude of rise in T (re) and the lag of response in T (re). During the stabilization stage before exercise, T (re) at 4 cm-depth was 0.5 degrees C lower than T (re) at 16 cm-depth (p < 0.05). As the depth measured in the rectum was shallower, the rise in T (re) during exercise was greater. However the rise in T (re) at 10, 13, 16 and 19 cm showed no systemic difference. Among seven depths, T (re) at 16 cm-depth had the most stable feature with the longest latent period (3.1 +/- 1.3 min) and the smallest rise (0.8 +/- 0.3 degrees C), while T (re) at 4 cm-depth was the most responsive to the change of exercise and rest with the shortest latent period (1.0 +/- 0.6 min) and the greatest rise (1.2 +/- 0.5 degrees C). The differences observed in the depths from 4 to 19 cm were offset by exercise to some extent. In summary, T (re) appeared in different manners according to the seven depths during the repetition of exercise and rest, but T (re) deeper than 10 cm-depth seemed to have no systematic differences.