Targeted temperature management (TTM) with therapeutic hypothermia (TH) during aortic arch surgery requires valid estimations of core body temperature. The ear canal and epitympanic region might be an easy-to-assess, noninvasive site for the read-out of supra-aortic, cerebral temperature. This observational cohort study comparatively investigated in-ear temperature and different core body temperature (cBT) measurements during TTM/TH for moderate hypothermic circulatory arrest (mHCA) in aortic arch surgery. In total 24 patients (mean age of 56.8 ± 17.5 years; six females) were measured using infrared-thermography of the epitympanic region (BT
tym
), thermistor-based measurements at the esophagus (BT
eso
; gold standard), at the ear canal (BT
ear
), at the nasopharynx (BT
nas
), in the bladder (BT
ves
), and in the rectum (BT
rec
). The data analysis comprised absolute agreement (AA), bias, intraclass correlation coefficient (ICC), and limit of agreement (LoA). The results revealed high AAs of BT
tym
, BT
ear
, BT
nas
in reference to BT
eso
(biases 0.3–0.6 °C), with also excellent ICCs > 0.9. BT
ves
and BT
rec
showed lower AAs, higher biases of + 2.5 °C to 3.1 °C with moderate ICCs during mHCA. In the phases of rapid temperature changes, the biases and LoAs were higher throughout all BT measurements. Herein, BT
tym
performed best of all measurement sites. The study informs about the BT dynamics at different body sites during the mHCA procedure. It supports the approach of using minimally invasive in-ear techniques to estimate core body temperature in an intrahospital TTM/TH setting of mHCA.
