The study of circadian rhythms in the human body using temperature measurements is the most informative way to assess the viability of the body’s rhythm-organizing systems. Pathological processes can affect circadian rhythm dynamics in damaged organs. Severe brain damage that caused the development of disorders of consciousness (DOC) (strokes, traumatic brain injury) disrupts the activity of central oscillators, by directly damaging or destroying the periphery links, and the level of preservation of circadian rhythms and the dynamics of their recovery can be informative diagnostic criteria for patient’s condition assessment. This study examined 23 patients with DOC by using a non-invasive method for obtaining body and cerebral cortex temperature to compare with healthy controls. Measurements were made with a 4 h interval for 52 h beginning at 08:00 on day 1 and ending at 08:00 on day 3. The profile of patients with DOC showed complete disruption compared to healthy controls with rhythmic patterns. The results indicate that the mechanisms for maintaining brain circadian rhythms are different from general homeostasis regulation of the body. Use of microwave radio thermometry for the identification of rehabilitation potential in patients with DOC is a promising area of investigation.