Continuous recordings of core body temperature (CBT) are a well-established approach in describing circadian rhythms. Given the discomfort of invasive CBT measurement techniques, the use of skin temperature recordings has been proposed as a surrogate. More recently, we proposed a heat-flux approach (the so-called Double Sensor) for monitoring CBT. Studies investigating the reliability of the heat-flux approach over a 24-hour period, as well as comparisons with skin temperature recordings, are however lacking. The first aim of the study was therefore to compare rectal, skin, and heat-flux temperature recordings for monitoring circadian rhythm. In addition, to assess the optimal placement of sensor probes, we also investigated the effect of different anatomical measurement sites, i.e. sensor probes positioned at the forehead vs. the sternum. Data were collected as part of the Berlin BedRest study (BBR2-2) under controlled, standardized, and thermoneutral conditions. 24-hours temperature data of seven healthy males were collected after 50 days of -6° head-down tilt bed-rest. Mean Pearson correlation coefficients indicated a high association between rectal and forehead temperature recordings (r > 0.80 for skin and Double Sensor). In contrast, only a poor to moderate relationship was observed for sensors positioned at the sternum (r = -0.02 and r = 0.52 for skin and Double Sensor, respectively). Cross-correlation analyses further confirmed the feasibility of the forehead as a preferred monitoring site. The phase difference between forehead Double Sensor and rectal recordings was not statistically different from zero (p = 0.313), and was significantly smaller than the phase difference between forehead skin and rectal temperatures (p = 0.016). These findings were substantiated by cosinor analyses, revealing significant differences for mesor, amplitude, and acrophase between rectal and forehead skin temperature recordings, but not between forehead Double Sensor and rectal temperature measurements. Finally, Bland-Altman analysis indicated narrower limits of agreement for rhythm parameters between rectal and Double Sensor measurements compared to between rectal and skin recordings, irrespective of the measurement site (i.e. forehead, sternum). Based on these data we conclude that (1) Double Sensor recordings are significantly superior to skin temperature measurements for non-invasively assessing the circadian rhythm of rectal temperature, and (2) temperature rhythms from the sternum are less reliable than from the forehead. We suggest that forehead Double Sensor recordings may provide a surrogate for rectal temperature in circadian rhythm research, where constant routine protocols are applied. Future studies will be needed to assess the sensor's ecological validity outside the laboratory under changing environmental and physiological conditions.