Core body temperature (Tc) is increasingly used as a biomarker of the fitness of an animal to its environment. Periodogram and cosinor analysis can be used to estimate the characteristics of the circadian rhythm of Tc. The sampling interval can be manipulated to maximise the recording period of loggers, but the impact of interval on the output of periodogram or cosinor analysis is unknown. Basic guidelines are available from signal analysis theory, but have never been tested on Tc data. We obtained data at 1-, 5-, or 10-minute intervals from nine avian or mammalian species, and re-sampled those data to simulate logging at up to 240-minute interval. The period of the rhythm was first analysed using the Lomb-Scargle periodogram, and the mesor, amplitude, acrophase, and adjusted coefficient of determination (R2) from the original and the re-sampled data were obtained using cosinor analysis. Sampling intervals longer than 60 minutes did not affect the average mesor, amplitude, acrophase, or adjusted R2, but did impact the period of the rhythm. In most species, the period was not detectable when intervals longer than 120 minutes were used. In all individual profiles, a 30-minute sampling interval modified the values of the mesor and amplitude by less than 0.1°C, and the adjusted R2 by less than 0.1. At a 30-minute interval, the acrophase was accurate to within 15 minutes for all species except mice. In most cases, a 30-minute sampling interval provides a reliable balance between parameter accuracy and logger longevity.