OBJECTIVE To compare rectal versus axillary temperatures in dogs and cats. METHODS Prospective observational study. METHODS 94 dogs and 31 cats. METHODS Paired axillary and rectal temperatures were measured in random order with a standardized method. Animal signalment, initial complaint, blood pressure, blood lactate concentration, and variables associated with vascular perfusion and coat were evaluated for associations with axillary and rectal temperatures. RESULTS Axillary temperature was positively correlated with rectal temperature (ρ = 0.75 in both species). Median axillary temperature (38.4°C [101.1°F] in dogs, and 38.4°C [101.2°F] in cats) was significantly different from median rectal temperature in dogs (38.9°C [102.0°F]) but not in cats (38.6°C [101.5°F]). Median rectal-axillary gradient (difference) was 0.4°C (0.7°F; range, -1.3° to 2.3°C [-2.4° to 4.1°F]) in dogs and 0.17°C (0.3°F; range -1.1° to 1.6°C [-1.9° to 3°F]) in cats. Sensitivity and specificity for detection of hyperthermia with axillary temperature were 57% and 100%, respectively, in dogs and 33% and 100%, respectively, in cats; sensitivity and specificity for detection of hypothermia were 86% and 87%, respectively, in dogs and 80% and 96%, respectively, in cats. Body weight (ρ = 0.514) and body condition score (ρ = 0.431) were correlated with rectal-axillary gradient in cats. CONCLUSIONS Although axillary and rectal temperatures were correlated in dogs and cats, a large gradient was present between rectal temperature and axillary temperature, suggesting that axillary temperature should not be used as a substitute for rectal temperature.