Objective: We retrospectively performed a comparative analysis of temperature measurement sites during surgical repair of the thoracic aorta. Methods: Between January 2004 and May 2006, 22 patients (mean age: 63 +/- 12 years) underwent operations on the thoracic aorta with arterial cannulation of the aortic arch concavity and selective antegrade cerebral perfusion (ACP) during deep hypothermic circulatory arrest (HCA). Indications for surgical intervention were acute type A dissection in 14 (64%) patients, degenerative aneurysm in 6 (27%), aortic infiltration of thymic carcinoma in 1 (4.5%) and intra-aortic stent refixation in 1 (4.5%). Rectal, tympanic and bladder temperatures were evaluated to identify the best reference to arterial blood temperature during HCA and ACP. Results: There were no operative deaths and the 30-day mortality rate was 13% (three patients). Permanent neurological deficits were not observed and transient changes occurred in two patients (9%). During re-warming, there was strong correlation between tympanic and arterial blood temperatures (r= 0.9541, p<0.001), in contrast to the rectal and bladder temperature (r=0.7654, p= n.s; r=0.7939, p= n.s., respectively). Conclusion: We conclude that tympanic temperature measurements correlate with arterial blood temperature monitoring during aortic surgery with HCA and ACP and, therefore, should replace bladder and rectal measurements.