The Cryogenic Sapphire Oscillator (CSO) is today recognized for its unprecedented frequency stability, mainly coming from the exceptional physical properties of its resonator made in a high-quality sapphire crystal. With these instruments, the fractional frequency measurement resolution, currently of the order of 10−16, is such that it is possible to detect very small phenomena such as residual resonator environmental sensitivities. Thus, we highlighted an unexpected magnetic sensitivity of the CSO at low magnetic fields. The fractional frequency sensitivity has been preliminarily evaluated to be 10−13/G, making this phenomenon a potential cause of frequency stability limitations. In this paper, we report the experimental data related to the magnetic sensitivity of the quasi-transverse magnetic Whispering Gallery (WGH) modes excited in sapphire crystals differing from their paramagnetic contaminant concentration. The magnetic behavior of the WGH modes does not follow the expected theory combining the Curie law and the Zeeman effect affecting the electron spin resonance of the paramagnetic ions present in the crystal.