Rectal (T(re)), ear canal (T(ear)) and esophageal (T(es)) temperatures have been used in the literature as core temperature indices in humans. The aim of the study was to investigate if localized lower body cooling would have a different effect on each of these measurements. We hypothesized that prolonged lower body surface cooling will result in a localized cooling effect for the rectal temperature not reflected in the other core measurement sites. Twelve participants (mean ± SD; 26.8 ± 6.0 years; 82.6 ± 13.9 kg; 179 ± 10 cm, BSA = 2.00 ± 0.21 m(2)) attended one experimental session consisting of sitting on a rubberized raft floor surface suspended in 5 °C water in a thermoneutral air environment (approximately 21.5 ± 0.5 °C). Experimental conditions were (a) a baseline phase during which participants were seated for 15 min in an upright position on an insulated pad (1.408 K ⋅ m(2) ⋅ W(-1)); (b) a cooling phase during which participants were exposed to the cooling surface for 2 h, and (c) an insulation phase during which the baseline condition was repeated for 1 h. Temperature data were collected at 1 Hz, reduced to 1 min averages, and transformed from absolute values to a change in temperature from baseline (15 min average). Metabolic data were collected breath-by-breath and integrated over the same temperature epoch. Within the baseline phase no significant change was found between the three indices of core temperature. By the end of the cooling phase, T(re) was significantly lower (Δ = -1.0 ± 0.4 °C) from baseline values than from T(ear) (Δ = -0.3 ± 0.3 °C) and T(es) (Δ = -0.1 ± 0.3 °C). T(re) continued to decrease during the insulation phase from Δ -1.0 ± 0.4 °C to as low as Δ -1.4 ± 0.5 °C. By the end of the insulation phase T(re) had slightly risen back to Δ -1.3 ± 0.4 °C but remained significantly different from baseline values and from the other two core measures. Metabolic data showed no variation throughout the experiment. In conclusion, the local cooling of the buttock area results in a drop in rectal temperature compromising the validity of the rectal temperature as a core temperature index under these conditions.